Isolated human kinase proteins, nucleic acid molecules encoding human kinase proteins, and uses thereof

ABSTRACT

The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the kinase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the kinase peptides, and methods of identifying modulators of the kinase peptides.

This case is a divisional of case Ser. No. 10/109,854, filed Apr. 1, 2002, issued as U.S. Pat. No. 6,630,337, which claims priority to divisional case Ser. No. 09/810,671, filed Mar. 19, 2001 issues as U.S. Pat. No. 6,455,291, which claims priority to U.S. Provisional Application No. 60/227,470, filed Aug. 24, 2000 now abandoned.

FIELD OF THE INVENTION

The present invention is in the field of kinase proteins that are related to the serine-arginine-rich protein kinase subfamily, recombinant DNA molecules, and protein production. The present invention specifically provides novel peptides and proteins that effect protein phosphorylation and nucleic acid molecules encoding such peptide and protein molecules, all of which are useful in the development of human therapeutics and diagnostic compositions and methods.

BACKGROUND OF THE INVENTION

Protein Kinases

Kinases regulate many different cell proliferation, differentiation, and signaling processes by adding phosphate groups to proteins. Uncontrolled signaling has been implicated in a variety of disease conditions including inflammation, cancer, arteriosclerosis, and psoriasis. Reversible protein phosphorylation is the main strategy for controlling activities of eukaryotic cells. It is estimated that more than 1000 of the 10,000 proteins active in a typical mammalian cell are phosphorylated. The high energy phosphate, which drives activation, is generally transferred from adenosine triphosphate molecules (ATP) to a particular protein by protein kinases and removed from that protein by protein phosphatases. Phosphorylation occurs in response to extracellular signals (hormones, neurotransmitters, growth and differentiation factors, etc), cell cycle checkpoints, and environmental or nutritional stresses and is roughly analogous to turning on a molecular switch. When the switch goes on, the appropriate protein kinase activates a metabolic enzyme, regulatory protein, receptor, cytoskeletal protein, ion channel or pump, or transcription factor.

The kinases comprise the largest known protein group, a superfamily of enzymes with widely varied functions and specificities. They are usually named after their substrate, their regulatory molecules, or some aspect of a mutant phenotype. With regard to substrates, the protein kinases may be roughly divided into two groups; those that phosphorylate tyrosine residues (protein tyrosine kinases, PTK) and those that phosphorylate serine or threonine residues (serine/threonine kinases, STK). A few protein kinases have dual specificity and phosphorylate threonine and tyrosine residues. Almost all kinases contain a similar 250-300 amino acid catalytic domain. The N-terminal domain, which contains subdomains I-IV, generally folds into a two-lobed structure, which binds and orients the ATP (or GTP) donor molecule. The larger C terminal lobe, which contains subdomains VI A-XI, binds the protein substrate and carries out the transfer of the gamma phosphate from ATP to the hydroxyl group of a serine, threonine, or tyrosine residue. Subdomain V spans the two lobes.

The kinases may be categorized into families by the different amino acid sequences (generally between 5 and 100 residues) located on either side of, or inserted into loops of, the kinase domain. These added amino acid sequences allow the regulation of each kinase as it recognizes and interacts with its target protein. The primary structure of the kinase domains is conserved and can be further subdivided into 11 subdomains. Each of the 11 subdomains contains specific residues and motifs or patterns of amino acids that are characteristic of that subdomain and are highly conserved (Hardie, G. and Hanks, S. (1995) The Protein Kinase Facts Books, Vol I:7-20 Academic Press, San Diego, Calif.).

The second messenger dependent protein kinases primarily mediate the effects of second messengers such as cyclic AMP (cAMP), cyclic GMP, inositol triphosphate, phosphatidylinositol, 3,4,5-triphosphate, cyclic-ADPribose, arachidonic acid, diacylglycerol and calcium-calmodulin. The cyclic-AMP dependent protein kinases (PKA) are important members of the STK family. Cyclic-AMP is an intracellular mediator of hormone action in all prokaryotic and animal cells that have been studied. Such hormone-induced cellular responses include thyroid hormone secretion, cortisol secretion, progesterone secretion, glycogen breakdown, bone resorption, and regulation of heart rate and force of heart muscle contraction. PKA is found in all animal cells and is thought to account for the effects of cyclic-AMP in most of these cells. Altered PKA expression is implicated in a variety of disorders and diseases including cancer, thyroid disorders, diabetes, atherosclerosis, and cardiovascular disease (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, New York, N.Y., pp. 416-431, 1887).

Calcium-calmodulin (CaM) dependent protein kinases are also members of STK family. Calmodulin is a calcium receptor that mediates many calcium regulated processes by binding to target proteins in response to the binding of calcium. The principle target protein in these processes is CaM dependent protein kinases. CaM-kinases are involved in regulation of smooth muscle contraction (MLC kinase), glycogen breakdown (phosphorylase kinase), and neurotransmission (CaM kinase I and CaM kinase II). CaM kinase I phosphorylates a variety of substrates including the neurotransmitter related proteins synapsin I and II, the gene transcription regulator, CREB, and the cystic fibrosis conductance regulator protein, CFTR (Haribabu, B. et al. (1995) EMBO Journal 14:3679-86). CaM II kinase also phosphorylates synapsin at different sites, and controls the synthesis of catecholamines in the brain through phosphorylation and activation of tyrosine hydroxylase. Many of the CaM kinases are activated by phosphorylation in addition to binding to CaM. The kinase may autophosphorylate itself, or be phosphorylated by another kinase as part of a “kinase cascade”.

Another ligand-activated protein kinase is 5′-AMP-activated protein kinase (AMPK) (Gao, G. et al. (1996) J. Biol Chem. 15:8675-81). Mammalian AMPK is a regulator of fatty acid and sterol synthesis through phosphorylation of the enzymes acetyl-CoA carboxylase and hydroxymethylglutaryl-CoA reductase and mediates responses of these pathways to cellular stresses such as heat shock and depletion of glucose and ATP. AMPK is a heterotrimeric complex comprised of a catalytic alpha subunit and two non-catalytic beta and gamma subunits that are believed to regulate the activity of the alpha subunit. Subunits of AMPK have a much wider distribution in non-lipogenic tissues such as brain, heart, spleen, and lung than expected. This distribution suggests that its role may extend beyond regulation of lipid metabolism alone.

The mitogen-activated protein kinases (MAP) are also members of the STK family. MAP kinases also regulate intracellular signaling pathways. They mediate signal transduction from the cell surface to the nucleus via phosphorylation cascades. Several subgroups have been identified, and each manifests different substrate specificities and responds to distinct extracellular stimuli (Egan, S. E. and Weinberg, R. A. (1993) Nature 365:781-783). MAP kinase signaling pathways are present in mammalian cells as well as in yeast. The extracellular stimuli that activate mammalian pathways include epidermal growth factor (EGF), ultraviolet light, hyperosmolar medium, heat shock, endotoxic lipopolysaccharide (LPS), and pro-inflammatory cytokines such as tumor necrosis factor (TNF) and interleukin-1 (IL-1).

PRK (proliferation-related kinase) is a serum/cytokine inducible STK that is involved in regulation of the cell cycle and cell proliferation in human megakaroytic cells (Li, B. et al. (1996) J. Biol. Chem. 271:19402-8). PRK is related to the polo (derived from humans polo gene) family of STKs implicated in cell division. PRK is downregulated in lung tumor tissue and may be a proto-oncogene whose deregulated expression in normal tissue leads to oncogenic transformation. Altered MAP kinase expression is implicated in a variety of disease conditions including cancer, inflammation, immune disorders, and disorders affecting growth and development.

The cyclin-dependent protein kinases (CDKs) are another group of STKs that control the progression of cells through the cell cycle. Cyclins are small regulatory proteins that act by binding to and activating CDKs that then trigger various phases of the cell cycle by phosphorylating and activating selected proteins involved in the mitotic process. CDKs are unique in that they require multiple inputs to become activated. In addition to the binding of cyclin, CDK activation requires the phosphorylation of a specific threonine residue and the dephosphorylation of a specific tyrosine residue.

Protein tyrosine kinases, PTKs, specifically phosphorylate tyrosine residues on their target proteins and may be divided into transmembrane, receptor PTKs and nontransmembrane, non-receptor PTKs. Transmembrane protein-tyrosine kinases are receptors for most growth factors. Binding of growth factor to the receptor activates the transfer of a phosphate group from ATP to selected tyrosine side chains of the receptor and other specific proteins. Growth factors (GF) associated with receptor PTKs include; epidermal GF, platelet-derived GF, fibroblast GF, hepatocyte GF, insulin and insulin-like GFs, nerve GF, vascular endothelial GF, and macrophage colony stimulating factor.

Non-receptor PTKs lack transmembrane regions and, instead, form complexes with the intracellular regions of cell surface receptors. Such receptors that function through non-receptor PTKs include those for cytokines, hormones (growth hormone and prolactin) and antigen-specific receptors on T and B lymphocytes.

Many of these PTKs were first identified as the products of mutant oncogenes in cancer cells where their activation was no longer subject to normal cellular controls. In fact, about one third of the known oncogenes encode PTKs, and it is well known that cellular transformation (oncogenesis) is often accompanied by increased tyrosine phosphorylation activity (Carbonneau H and Tonks NK (1992) Annu. Rev. Cell. Biol. 8:463-93). Regulation of PTK activity may therefore be an important strategy in controlling some types of cancer.

The phosphorylation of proteins on serine/threonine and/or tyrosine residues is now well established as a principal mechanism in the control of many cellular functions, such as the cell cycle, differentiation and signal transduction. Serine/threonine protein kinases add phosphate moiety to a serine or threonine residue of the substrate. Protein kinase substrates include elements of signal transduction pathway such as transcription factors or ion channels, as well as structural proteins such as filaments and cellular motors. Family of protein kinases is one of the largest in the genome. Classification of kinases is based on their sequence, tissue localization and domain topology.

Primary structures of kinases are rather conserved; functional prediction based on the sequence alone is difficult. A number of soluble and transmembrane proteins contain kinase domains along with other structural components; these multi-domain proteins are often referred to as kinases. Because of this additional information, multi-domain kinases are easier to classify. Tissue specific expression of kinases is often defined by transcription regulatory elements.

Serine- and arginine-rich (SR) proteins were originally characterized by a shared epitope that cross-reacts with the monoclonal antibody mAb104, at least one N-terminal RNA recognition motif and a basic C-terminal domain rich in serine and arginine residues, often arranged in tandem repeats. Since that time, many more potential SR proteins or SR-like proteins have been identified using different monoclonal antibodies, so that the number of such proteins may well reach 80 or more. There is evidence that the SR domain is involved in protein-protein interactions as well as protein-RNA interactions, and may serve as a localization signal directing proteins to nuclear speckles

The kinase of the present invention is similar to Serine- and arginine-rich (SR) or CDC like kinase 4, which is involved in cell cycle control. CDC like kinase 4 is one of the serine-arginine-rich (SR) protein kinases. The substrates of these enzymes include the components of splicing machinery. By changing their substrates' phosphorylation states, they affect these proteins' activities and intracellular distribution. As a result of modification, their substrates may select different splice sites, which results in alternative splice variants. CLK and SRPK are the two notable examples of SR kinases. CLK is involved in regulation of splicing, like most of SR kinases, while SRPK phosphorylates protamine, a small basic arginine-rich protein that replaces histamine in developing spermatozoa. Unlike other SR kinases, SRPK is localized in cytoplasm and expressed predominantly in germ cells.

The human CDC like kinase 4 gene of the present invention can be expressed in yeast to identify possible interactors; this can be done by means of a complementation assay or a two-hybrid experiment. Artificially synthesized enzyme as well as derived peptides can be used to activate or inhibit cellular processes modulated by this kinase. Immunoassay or PCR may be used to measure the concentration of this protein and detect abnormally developing tissue or cancerous growth.

For a review of serine-arginine-rich (SR) protein kinases and CDC like kinase 4, see the references of Nayler et al. Biochem J Sep. 15, 1997; 326 (Pt 3):693-700, Colwill et al., EMBO J Jan. 15, 1996; 15(2):265-75, Papoutsopoulou et al., Nucleic Acids Res Jul. 15, 1999; 27(14):2972-80.

Kinase proteins; particularly members of the serine-arginine-rich protein kinase subfamily, are a major target for drug action and development. Accordingly, it is valuable to the field of pharmaceutical development to identify and characterize previously unknown members of this subfamily of kinase proteins. The present invention advances the state of the art by providing previously unidentified human kinase proteins that have homology to members of the serine-arginine-rich protein kinase subfamily.

SUMMARY OF THE INVENTION

The present invention is based in part on the identification of amino acid sequences of human kinase peptides and proteins that are related to the serine-arginine-rich protein kinase subfamily, as well as allelic variants and other mammalian orthologs thereof. These unique peptide sequences, and nucleic acid sequences that encode these peptides, can be used as models for the development of human therapeutic targets, aid in the identification of therapeutic proteins, and serve as targets for the development of human therapeutic agents that modulate kinase activity in cells and tissues that express the kinase. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte.

DESCRIPTION OF THE FIGURE SHEETS

FIGS. 1A-1B provide the nucleotide sequence of a cDNA molecule or transcript sequence that encodes the kinase protein of the present invention. (SEQ ID NO:1) In addition, structure and functional information is provided, such as ATG start, stop and tissue distribution, where available, that allows one to readily determine specific uses of inventions based on this molecular sequence. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte.

FIGS. 2A-2D provide the predicted amino acid sequence of the kinase of the present invention. (SEQ ID NO:2) In addition structure and functional information such as protein family, function, and modification sites is provided where available, allowing one to readily determine specific uses of inventions based on this molecular sequence.

FIGS. 3A-3J provide genomic sequences that span the gene encoding the kinase protein of the present invention. (SEQ ID NO:3) In addition structure and functional information, such as intron/exon structure, promoter location, etc., is provided where available, allowing one to readily determine specific uses of inventions based on this molecular sequence. As illustrated in FIG. 3, SNPs, including insertion/deletion variants (“indels”), were identified at 10 different nucleotide positions.

DETAILED DESCRIPTION OF THE INVENTION

General Description

The present invention is based on the sequencing of the human genome. During the sequencing and assembly of the human genome, analysis of the sequence information revealed previously unidentified fragments of the human genome that encode peptides that share structural and/or sequence homology to protein/peptide/domains identified and characterized within the art as being a kinase protein or part of a kinase protein and are related to the serine-arginine-rich protein kinase subfamily. Utilizing these sequences, additional genomic sequences were assembled and transcript and/or cDNA sequences were isolated and characterized. Based on this analysis, the present invention provides amino acid sequences of human kinase peptides and proteins that are related to the serine-arginine-rich protein kinase subfamily, nucleic acid sequences in the form of transcript sequences, cDNA sequences and/or genomic sequences that encode these kinase peptides and proteins, nucleic acid variation (allelic information), tissue distribution of expression, and information about the closest art known protein/peptide/domain that has structural or sequence homology to the kinase of the present invention.

In addition to being previously unknown, the peptides that are provided in the present invention are selected based on their ability to be used for the development of commercially important products and services. Specifically, the present peptides are selected based on homology and/or structural relatedness to known kinase proteins of the serine-arginine-rich protein kinase subfamily and the expression pattern observed. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. The art has clearly established the commercial importance of members of this family of proteins and proteins that have expression patterns similar to that of the present gene. Some of the more specific features of the peptides of the present invention, and the uses thereof, are described herein, particularly in the Background of the Invention and in the annotation provided in the Figures, and/or are known within the art for each of the known serine-arginine-rich protein family or subfamily of kinase proteins.

Specific Embodiments

Peptide Molecules

The present invention provides nucleic acid sequences that encode protein molecules that have been identified as being members of the kinase family of proteins and are related to the serine-arginine-rich protein kinase subfamily (protein sequences are provided in FIG. 2, transcript/cDNA sequences are provided in FIG. 1 and genomic sequences are provided in FIG. 3). The peptide sequences provided in FIG. 2, as well as the obvious variants described herein, particularly allelic variants as identified herein and using the information in FIG. 3, will be referred herein as the kinase peptides of the present invention, kinase peptides, or peptides/proteins of the present invention.

The present invention provides isolated peptide and protein molecules that consist of, consist essentially of, or comprise the amino acid sequences of the kinase peptides disclosed in the FIG. 2, (encoded by the nucleic acid molecule shown in FIG. 1, transcript/cDNA or FIG. 3, genomic sequence), as well as all obvious variants of these peptides that are within the art to make and use. Some of these variants are described in detail below.

As used herein, a peptide is said to be “isolated” or “purified” when it is substantially free of cellular material or free of chemical precursors or other chemicals. The peptides of the present invention can be purified to homogeneity or other degrees of purity. The level of purification will be based on the intended use. The critical feature is that the preparation allows for the desired function of the peptide, even if in the presence of considerable amounts of other components (the features of an isolated nucleic acid molecule is discussed below).

In some uses, “substantially free of cellular material” includes preparations of the peptide having less than about 30% (by dry weight) other proteins (i.e., contaminating protein), less than about 20% other proteins, less than about 10% other proteins, or less than about 5% other proteins. When the peptide is recombinantly produced, it can also be substantially free of culture medium, i.e., culture medium represents less than about 20% of the volume of the protein preparation.

The language “substantially free of chemical precursors or other chemicals” includes preparations of the peptide in which it is separated from chemical precursors or other chemicals that are involved in its synthesis. In one embodiment, the language “substantially free of chemical precursors or other chemicals” includes preparations of the kinase peptide having less than about 30% (by dry weight) chemical precursors or other chemicals, less than about 20% chemical precursors or other chemicals, less than about 10% chemical precursors or other chemicals, or less than about 5% chemical precursors or other chemicals.

The isolated kinase peptide can be purified from cells that naturally express it, purified from cells that have been altered to express it (recombinant), or synthesized using known protein synthesis methods. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. For example, a nucleic acid molecule encoding the kinase peptide is cloned into an expression vector, the expression vector introduced into a host cell and the protein expressed in the host cell. The protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques. Many of these techniques are described in detail below.

Accordingly, the present invention provides proteins that consist of the amino acid sequences provided in FIG. 2 (SEQ ID NO:2), for example, proteins encoded by the transcript/cDNA nucleic acid sequences shown in FIG. 1 (SEQ ID NO:1) and the genomic sequences provided-in FIG. 3 (SEQ ID NO:3). The amino acid sequence of such a protein is provided in FIG. 2. A protein consists of an amino acid sequence when the amino acid sequence is the final amino acid sequence of the protein.

The present invention further provides proteins that consist essentially of the amino acid sequences provided in FIG. 2 (SEQ ID NO:2), for example, proteins encoded by the transcript/cDNA nucleic acid sequences shown in FIG. 1 (SEQ ID NO:1) and the genomic sequences provided in FIG. 3 (SEQ ID NO:3). A protein consists essentially of an amino acid sequence when such an amino acid sequence is present with only a few additional amino acid residues, for example from about 1 to about 100 or so additional residues, typically from 1 to about 20 additional residues in the final protein.

The present invention further provides proteins that comprise the amino acid sequences provided in FIG. 2 (SEQ ID NO:2), for example, proteins encoded by the transcript/cDNA nucleic acid sequences shown in FIG. 1 (SEQ ID NO:1) and the genomic sequences provided in FIG. 3 (SEQ ID NO:3). A protein comprises an amino acid sequence when the amino acid sequence is at least part of the final amino acid sequence of the protein. In such a fashion, the protein can be only the peptide or have additional amino acid molecules, such as amino acid residues (contiguous encoded sequence) that are naturally associated with it or heterologous amino acid residues/peptide sequences. Such a protein can have a few additional amino acid residues or can comprise several hundred or more additional amino acids. The preferred classes of proteins that are comprised of the kinase peptides of the present invention are the naturally occurring mature proteins. A brief description of how various types of these proteins can be made/isolated is provided below.

The kinase peptides of the present invention can be attached to heterologous sequences to form chimeric or fusion proteins. Such chimeric and fusion proteins comprise a kinase peptide operatively linked to a heterologous protein having an amino acid sequence not substantially homologous to the kinase peptide. “Operatively linked” indicates that the kinase peptide and the heterologous protein are fused in-frame. The heterologous protein can be fused to the N-terminus or C-terminus of the kinase peptide.

In some uses, the fusion protein does not affect the activity of the kinase peptide per se. For example, the fusion protein can include, but is not limited to, enzymatic fusion proteins, for example beta-galactosidase fusions, yeast two-hybrid GAL fusions, poly-His fusions, MYC-tagged, HI-tagged and Ig fusions. Such fusion proteins, particularly poly-His fusions, can facilitate the purification of recombinant kinase peptide. In certain host cells (e.g., mammalian host cells), expression and/or secretion of a protein can be increased by using a heterologous signal sequence.

A chimeric or fusion protein can be produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different protein sequences are ligated together in-frame in accordance with conventional techniques. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and re-amplified to generate a chimeric gene sequence (see Ausubel et al., Current Protocols in Molecular Biology, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST protein). A kinase peptide-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the kinase peptide.

As mentioned above, the present invention also provides and enables obvious variants of the amino acid sequence of the proteins of the present invention, such as naturally occurring mature forms of the peptide, allelic/sequence variants of the peptides, non-naturally occurring recombinantly derived variants of the peptides, and orthologs and paralogs of the peptides. Such variants can readily be generated using art-known techniques in the fields of recombinant nucleic acid technology and protein biochemistry. It is understood, however, that variants exclude any amino acid sequences disclosed prior to the invention.

Such variants can readily be identified/made using molecular techniques and the sequence information disclosed herein. Further, such variants can readily be distinguished from other peptides based on sequence and/or structural homology to the kinase peptides of the present invention. The degree of homology/identity present will be based primarily on whether the peptide is a functional variant or non-functional variant, the amount of divergence present in the paralog family and the evolutionary distance between the orthologs.

To determine the percent identity of two amino acid sequences or two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, at least 30%, 40%, 50%, 60%, 70%, 80%, or 90% or more of the length of a reference sequence is aligned for comparison purposes. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.

The comparison of sequences and determination of percent identity and similarity between two sequences can be accomplished using a mathematical algorithm. (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991). In a preferred embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (Devereux, J., et al., Nucleic Acids Res. 12(1):387 (1984)) (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Myers and W. Miller (CABIOS, 4:11-17 (1989)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.

The nucleic acid and protein sequences of the present invention can further be used as a “query sequence” to perform a search against sequence databases to, for example, identify other family members or related sequences. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (J. Mol. Biol. 215:403-10 (1990)). BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to the nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to the proteins of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al. (Nucleic Acids Res. 25(17):3389-3402 (1997)). When utilizing BLAST and gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used.

Full-length pre-processed forms, as well as mature processed forms, of proteins that comprise one of the peptides of the present invention can readily be identified as having complete sequence identity to one of the kinase peptides of the present invention as well as being encoded by the same genetic locus as the kinase peptide provided herein. As indicated by the data presented in FIG. 3, the map position was determined to be on chromosome 5 by ePCR.

Allelic variants of a kinase peptide can readily be identified as being a human protein having a high degree (significant) of sequence homology/identity to at least a portion of the kinase peptide as well as being encoded by the same genetic locus as the kinase peptide provided herein. Genetic locus can readily be determined based on the genomic information provided in FIG. 3, such as the genomic sequence mapped to the reference human. As indicated by the data presented in FIG. 3, the map position was determined to be on chromosome 5 by ePCR. As used herein, two proteins (or a region of the proteins) have significant homology when the amino acid sequences are typically at least about 70-80%, 80-90%, and more typically at least about 90-95% or more homologous. A significantly homologous amino acid sequence, according to the present invention, will be encoded by a nucleic acid sequence that will hybridize to a kinase peptide encoding nucleic acid molecule under stringent conditions as more fully described below.

FIG. 3 provides information on SNPs that have been found in the gene encoding the transporter protein of the present invention. SNPs were identified at 10 different nucleotide positions in introns and regions 5′ and 3′ of the ORF. Such SNPs in introns and outside the ORF may affect control/regulatory elements.

Paralogs of a kinase peptide can readily be identified as having some degree of significant sequence homology/identity to at least a portion of the kinase peptide, as being encoded by a gene from humans, and as having similar activity or function. Two proteins will typically be considered paralogs when the amino acid sequences are typically at least about 60% or greater, and more typically at least about 70% or greater homology through a given region or domain. Such paralogs will be encoded by a nucleic acid sequence that will hybridize to a kinase peptide encoding nucleic acid molecule under moderate to stringent conditions as more fully described below.

Orthologs of a kinase peptide can readily be identified as having some degree of significant sequence homology/identity to at least a portion of the kinase peptide as well as being encoded by a gene from another organism. Preferred orthologs will be isolated from mammals, preferably primates, for the development of human therapeutic targets and agents. Such orthologs will be encoded by a nucleic acid sequence that will hybridize to a kinase peptide encoding nucleic acid molecule under moderate to stringent conditions, as more fully described below, depending on the degree of relatedness of the two organisms yielding the proteins.

Non-naturally occurring variants of the kinase peptides of the present invention can readily be generated using recombinant techniques. Such variants include, but are not limited to deletions, additions and substitutions in the amino acid sequence of the kinase peptide. For example, one class of substitutions are conserved amino acid substitution. Such substitutions are those that substitute a given amino acid in a kinase peptide by another amino acid of like characteristics. Typically seen as conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu, and Ile; interchange of the hydroxyl residues Ser and Thr; exchange of the acidic residues Asp and Glu; substitution between the amide residues Asn and Gln; exchange of the basic residues Lys and Arg; and replacements among the aromatic residues Phe and Tyr. Guidance concerning which amino acid changes are likely to be phenotypically silent are found in Bowie et al., Science 247:1306-1310 (1990).

Variant kinase peptides can be fully functional or can lack function in one or more activities, e.g. ability to bind substrate, ability to phosphorylate substrate, ability to mediate signaling, etc. Fully functional variants typically contain only conservative variation or variation in non-critical residues or in non-critical regions. FIG. 2 provides the result of protein analysis and can be used to identify critical domains/regions. Functional variants can also contain substitution of similar amino acids that result in no change or an insignificant change in function. Alternatively, such substitutions may positively or negatively affect function to some degree.

Non-functional variants typically contain one or more non-conservative amino acid substitutions, deletions, insertions, inversions, or truncation or a substitution, insertion, inversion, or deletion in a critical residue or critical region.

Amino acids that are essential for function can be identified by methods known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham et al., Science 244:1081-1085 (1989)), particularly using the results provided in FIG. 2. The latter procedure introduces single alanine mutations at every residue in the molecule. The resulting mutant molecules are then tested for biological activity such as kinase activity or in assays such as an in vitro proliferative activity. Sites that are critical for binding partner/substrate binding can also be determined by structural analysis such as crystallization, nuclear magnetic resonance or photoaffinity labeling (Smith et al., J. Mol. Biol. 224:899-904 (1992); de Vos et al. Science 255:306-312 (1992)).

The present invention further provides fragments of the kinase peptides, in addition to proteins and peptides that comprise and consist of such fragments, particularly those comprising the residues identified in FIG. 2. The fragments to which the invention pertains, however, are not to be construed as encompassing fragments that may be disclosed publicly prior to the present invention.

As used herein, a fragment comprises at least 8, 10, 12, 14, 16, or more contiguous amino acid residues from a kinase peptide. Such fragments can be chosen based on the ability to retain one or more of the biological activities of the kinase peptide or could be chosen for the ability to perform a function, e.g. bind a substrate or act as an immunogen. Particularly important fragments are biologically active fragments, peptides that are, for example, about 8 or more amino acids in length. Such fragments will typically comprise a domain or motif of the kinase peptide, e.g., active site, a transmembrane domain or a substrate-binding domain. Further, possible fragments include, but are not limited to, domain or motif containing fragments, soluble peptide fragments, and fragments containing immunogenic structures. Predicted domains and functional sites are readily identifiable by computer programs well known and readily available to those of skill in the art (e.g., PROSITE analysis). The results of one such analysis are provided in FIG. 2.

Polypeptides often contain amino acids other than the 20 amino acids commonly referred to as the 20 naturally occurring amino acids. Further, many amino acids, including the terminal amino acids, may be modified by natural processes, such as processing and other post-translational modifications, or by chemical modification techniques well known in the art. Common modifications that occur naturally in kinase peptides are described in basic texts, detailed monographs, and the research literature, and they are well known to those of skill in the art (some of these features are identified in FIG. 2).

Known modifications include, but are not limited to, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.

Such modifications are well known to those of skill in the art and have been described in great detail in the scientific literature. Several particularly common modifications, glycosylation, lipid attachment, sulfation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation, for instance, are described in most basic texts, such as Proteins—Structure and Molecular Properties, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993). Many detailed reviews are available on this subject, such as by Wold, F., Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed., Academic Press, New York 1-12 (1983); Seifter et al. (Meth. Enzymol. 182: 626-646 (1990)) and Rattan et al. (Ann. N.Y. Acad. Sci. 663:48-62 (1992)).

Accordingly, the kinase peptides of the present invention also encompass derivatives or analogs in which a substituted amino acid residue is not one encoded by the genetic code, in which a substituent group is included, in which the mature kinase peptide is fused with another compound, such as a compound to increase the half-life of the kinase peptide (for example, polyethylene glycol), or in which the additional amino acids are fused to the mature kinase peptide, such as a leader or secretory sequence or a sequence for purification of the mature kinase peptide or a pro-protein sequence.

Protein/Peptide Uses

The proteins of the present invention can be used in substantial and specific assays related to the functional information provided in the Figures; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or its binding partner or ligand) in biological fluids; and as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state). Where the protein binds or potentially binds to another protein or ligand (such as, for example, in a kinase-effector protein interaction or kinase-ligand interaction), the protein can be used to identify the binding partner/ligand so as to develop a system to identify inhibitors of the binding interaction. Any or all of these uses are capable of being developed into reagent grade or kit format for commercialization as commercial products.

Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include “Molecular Cloning: A Laboratory Manual”, 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds., 1989, and “Methods in Enzymology: Guide to Molecular Cloning Techniques”, Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987.

The potential uses of the peptides of the present invention are based primarily on the source of the protein as well as the class/action of the protein. For example, kinases isolated from humans and their human/mammalian orthologs serve as targets for identifying agents for use in mammalian therapeutic applications, e.g. a human drug, particularly in modulating a biological or pathological response in a cell or tissue that expresses the kinase. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression/in leukocyte. A large percentage of pharmaceutical agents are being developed that modulate the activity of kinase proteins, particularly members of the serine-arginine-rich protein subfamily (see Background of the Invention). The structural and functional information provided in the Background and Figures provide specific and substantial uses for the molecules of the present invention, particularly in combination with the expression information provided in FIG. 1. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. Such uses can readily be determined using the information provided herein, that which is known in the art, and routine experimentation.

The proteins of the present invention (including variants and fragments that may have been disclosed prior to the present invention) are useful for biological assays related to kinases that are related to members of the serine-arginine-rich protein subfamily. Such assays involve any of the known kinase functions or activities or properties useful for diagnosis and treatment of kinase-related conditions that are specific for the subfamily of kinases that the one of the present invention belongs to, particularly in cells and tissues that express the kinase. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte.

The protein of the present invention is similar to CDC like kinase 4, which is involved in cell cycle control. CDC like kinase 4 is one of the so-called serine-arginine-rich (SR) protein kinases. The substrates of these enzymes include the components of splicing machinery. By changing their substrates' phosphorylation states, they affect these proteins' activities and intracellular distribution. As a result of modification, their substrates may select different splice sites, which results in alternative splice variants. CLK and SRPK are the two notable examples of SR kinases. CLK is involved in regulation of splicing, like most of SR kinases, while SRPK phosphorylates protamine, a small basic arginine-rich protein that replaces histamine in developing spermatozoa. Unlike other SR kinases, SRPK is localized in cytoplasm and expressed predominantly in germ cells.

The human CDC like kinase 4 gene of the present invention can be expressed in yeast to identify possible interactors; this can be done by means of a complementation assay or a two-hybrid experiment. Artificially synthesized enzyme as well as derived peptides can be used to activate or inhibit cellular processes modulated by this kinase. Immunoassay or PCR may be used to measure the concentration of this protein and detect abnormally developing tissue or cancerous growth.

The proteins of the present invention are also useful in drug screening assays, in cell-based or cell-free systems. Cell-based systems can be native, i.e., cells that normally express the kinase, as a biopsy or expanded in cell culture. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. In an alternate embodiment, cell-based assays involve recombinant host cells expressing the kinase protein.

The polypeptides can be used to identify compounds that modulate kinase activity of the protein in its natural state or an altered form that causes a specific disease or pathology associated with the kinase. Both the kinases of the present invention and appropriate variants and fragments can be used in high-throughput screens to assay candidate compounds for the ability to bind to the kinase. These compounds can be further screened against a functional kinase to determine the effect of the compound on the kinase activity. Further, these compounds can be tested in animal or invertebrate systems to determine activity/effectiveness. Compounds can be identified that activate (agonist) or inactivate (antagonist) the kinase to a desired degree.

Further, the proteins of the present invention can be used to screen a compound for the ability to stimulate or inhibit interaction between the kinase protein and a molecule that normally interacts with the kinase protein, e.g. a substrate or a component of the signal pathway that the kinase protein normally interacts (for example, another kinase). Such assays typically include the steps of combining the kinase protein with a candidate compound under conditions that allow the kinase protein, or fragment, to interact with the target molecule, and to detect the formation of a complex between the protein and the target or to detect the biochemical consequence of the interaction with the kinase protein and the target, such as any of the associated effects of signal transduction such as protein phosphorylation, cAMP turnover, and adenylate cyclase activation, etc.

Candidate compounds include, for example, 1) peptides such as soluble peptides, including Ig-tailed fusion peptides and members of random peptide libraries (see, e.g., Lam et al., Nature 354:82-84 (1991); Houghten et al., Nature 354:84-86 (1991)) and combinatorial chemistry-derived molecular libraries made of D- and/or L-configuration amino acids; 2) phosphopeptides (e.g., members of random and partially degenerate, directed phosphopeptide libraries, see, e.g., Songyang et al., Cell 72:767-778 (1993)); 3) antibodies (e.g., polyclonal, monoclonal, humanized, anti-idiotypic, chimeric, and single chain antibodies as well as Fab, F(ab′)₂, Fab expression library fragments, and epitope-binding fragments of antibodies); and 4) small organic and inorganic molecules (e.g., molecules obtained from combinatorial and natural product libraries).

One candidate compound is a soluble fragment of the receptor that competes for substrate binding. Other candidate compounds include mutant kinases or appropriate fragments containing mutations that affect kinase function and thus compete for substrate. Accordingly, a fragment that competes for substrate, for example with a higher affinity, or a fragment that binds substrate but does not allow release, is encompassed by the invention.

The invention further includes other end point assays to identify compounds that modulate (stimulate or inhibit) kinase activity. The assays typically involve an assay of events in the signal transduction pathway that indicate kinase activity. Thus, the phosphorylation of a substrate, activation of a protein, a change in the expression of genes that are up- or down-regulated in response to the kinase protein dependent signal cascade can be assayed.

Any of the biological or biochemical functions mediated by the kinase can be used as an endpoint assay. These include all of the biochemical or biochemical/biological events described herein, in the references cited herein, incorporated by reference for these endpoint assay targets, and other functions known to those of ordinary skill in the art or that can be readily identified using the information provided in the Figures, particularly FIG. 2. Specifically, a biological function of a cell or tissues that expresses the kinase can be assayed. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte.

Binding and/or activating compounds can also be screened by using chimeric kinase proteins in which the amino terminal extracellular domain, or parts thereof, the entire transmembrane domain or subregions, such as any of the seven transmembrane segments or any of the intracellular or extracellular loops and the carboxy terminal intracellular domain, or parts thereof, can be replaced by heterologous domains or subregions. For example, a substrate-binding region can be used that interacts with a different substrate then that which is recognized by the native kinase. Accordingly, a different set of signal transduction components is available as an end-point assay for activation. This allows for assays to be performed in other than the specific host cell from which the kinase is derived.

The proteins of the present invention are also useful in competition binding assays in methods designed to discover compounds that interact with the kinase (e.g. binding partners and/or ligands). Thus, a compound is exposed to a kinase polypeptide under conditions that allow the compound to bind or to otherwise interact with the polypeptide. Soluble kinase polypeptide is also added to the mixture. If the test compound interacts with the soluble kinase polypeptide, it decreases the amount of complex formed or activity from the kinase target. This type of assay is particularly useful in cases in which compounds are sought that interact with specific regions of the kinase. Thus, the soluble polypeptide that competes with the target kinase region is designed to contain peptide sequences corresponding to the region of interest.

To perform cell free drug screening assays, it is sometimes desirable to immobilize either the kinase protein, or fragment, or its target molecule to facilitate separation of complexes from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay.

Techniques for immobilizing proteins on matrices can be used in the drug screening assays. In one embodiment, a fusion protein can be provided which adds a domain that allows the protein to be bound to a matrix. For example, glutathione-S-transferase fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized microtitre plates, which are then combined with the cell lysates (e.g., ³⁵S-labeled) and the candidate compound, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads are washed to remove any unbound label, and the matrix immobilized and radiolabel determined directly, or in the supernatant after the complexes are dissociated. Alternatively, the complexes can be dissociated from the matrix, separated by SDS-PAGE, and the level of kinase-binding protein found in the bead fraction quantitated from the gel using standard electrophoretic techniques. For example, either the polypeptide or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin using techniques well known in the art. Alternatively, antibodies reactive with the protein but which do not interfere with binding of the protein to its target molecule can be derivatized to the wells of the plate, and the protein trapped in the wells by antibody conjugation. Preparations of a kinase-binding protein and a candidate compound are incubated in the kinase protein-presenting wells and the amount of complex trapped in the well can be quantitated. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the kinase protein target molecule, or which are reactive with kinase protein and compete with the target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the target molecule.

Agents that modulate one of the kinases of the present invention can be identified using one or more of the above assays, alone or in combination. It is generally preferable to use a cell-based or cell free system first and then confirm activity in an animal or other model system. Such model systems are well known in the art and can readily be employed in this context.

Modulators of kinase protein activity identified according to these drug screening assays can be used to treat a subject with a disorder mediated by the kinase pathway, by treating cells or tissues that express the kinase. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. These methods of treatment include the steps of administering a modulator of kinase activity in a pharmaceutical composition to a subject in need of such treatment, the modulator being identified as described herein.

In yet another aspect of the invention, the kinase proteins can be used as “bait proteins” in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; Iwabuchi et al. (1993) Oncogene 8:1693-1696; and Brent WO94/10300), to identify other proteins, which bind to or interact with the kinase and are involved in kinase activity. Such kinase-binding proteins are also likely to be involved in the propagation of signals by the kinase proteins or kinase targets as, for example, downstream elements of a kinase-mediated signaling pathway. Alternatively, such kinase-binding proteins are likely to be kinase inhibitors.

The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for a kinase protein is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct, a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein (“prey” or “sample”) is fused to a gene that codes for the activation domain of the known transcription factor. If the “bait” and the “prey” proteins are able to interact, in vivo, forming a kinase-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the kinase protein.

This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent identified as described herein in an appropriate animal model. For example, an agent identified as described herein (e.g., a kinase-modulating agent, an antisense kinase nucleic acid molecule, a kinase-specific antibody, or a kinase-binding partner) can be used in an animal or other model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal or other model to determine the mechanism of action of such an agent. Furthermore, this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.

The kinase proteins of the present invention are also useful to provide a target for diagnosing a disease or predisposition to disease mediated by the peptide. Accordingly, the invention provides methods for detecting the presence, or levels of, the protein (or encoding mRNA) in a cell, tissue, or organism. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. The method involves contacting a biological sample with a compound capable of interacting with the kinase protein such that the interaction can be detected. Such an assay can be provided in a single detection format or a multi-detection format such as an antibody chip array.

One agent for detecting a protein in a sample is an antibody capable of selectively binding to protein. A biological sample includes tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject.

The peptides of the present invention also provide targets for diagnosing active protein activity, disease, or predisposition to disease, in a patient having a variant peptide, particularly activities and conditions that are known for other members of the family of proteins to which the present one belongs. Thus, the peptide can be isolated from a biological sample and assayed for the presence of a genetic mutation that results in aberrant peptide. This includes amino acid substitution, deletion, insertion, rearrangement, (as the result of aberrant splicing events), and inappropriate post-translational modification. Analytic methods include altered electrophoretic mobility, altered tryptic peptide digest, altered kinase activity in cell-based or cell-free assay, alteration in substrate or antibody-binding pattern, altered isoelectric point, direct amino acid sequencing, and any other of the known assay techniques useful for detecting mutations in a protein. Such an assay can be provided in a single detection format or a multi-detection format such as an antibody chip array.

In vitro techniques for detection of peptide include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence using a detection reagent, such as an antibody or protein binding agent. Alternatively, the peptide can be detected in vivo in a subject by introducing into the subject a labeled anti-peptide antibody or other types of detection agent. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques. Particularly useful are methods that detect the allelic variant of a peptide expressed in a subject and methods which detect fragments of a peptide in a sample.

The peptides are also useful in pharmacogenomic analysis. Pharmacogenomics deal with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, e.g., Eichelbaum, M. (Clin. Exp. Pharmacol. Physiol. 23(10-11):983-985 (1996)), and Linder, M. W. (Clin. Chem. 43(2):254-266 (1997.) The clinical outcomes of these variations result in severe toxicity of therapeutic drugs in certain individuals or therapeutic failure of drugs in certain individuals as a result of individual variation in metabolism. Thus, the genotype of the individual can determine the way a therapeutic compound acts on the body or the way the body metabolizes the compound. Further, the activity of drug metabolizing enzymes effects both the intensity and duration of drug action. Thus, the pharmacogenomics of the individual permit the selection of effective compounds and effective dosages of such compounds for prophylactic or therapeutic treatment based on the individual's genotype. The discovery of genetic polymorphisms in some drug metabolizing enzymes has explained why some patients do not obtain the expected drug effects, show an exaggerated drug effect, or experience serious toxicity from standard drug dosages. Polymorphisms can be expressed in the phenotype of the extensive metabolizer and the phenotype of the poor metabolizer. Accordingly, genetic polymorphism may lead to allelic protein variants of the kinase protein in which one or more of the kinase functions in one population is different from those in another population. The peptides thus allow a target to ascertain a genetic predisposition that can affect treatment modality. Thus, in a ligand-based treatment, polymorphism may give rise to amino terminal extracellular domains and/or other substrate-binding regions that are more or less active in substrate binding, and kinase activation. Accordingly, substrate dosage would necessarily be modified to maximize the therapeutic effect within a given population containing a polymorphism. As an alternative to genotyping, specific polymorphic peptides could be identified.

The peptides are also useful for treating a disorder characterized by an absence of, inappropriate, or unwanted expression of the protein. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. Accordingly, methods for treatment include the use of the kinase protein or fragments.

Antibodies

The invention also provides antibodies that selectively bind to one of the peptides of the present invention, a protein comprising such a peptide, as well as variants and fragments thereof. As used herein, an antibody selectively binds a target peptide when it binds the target peptide and does not significantly bind to unrelated proteins. An antibody is still considered to selectively bind a peptide even if it also binds to other proteins that are not substantially homologous with the target peptide so long as such proteins share homology with a fragment or domain of the peptide target of the antibody. In this case, it would be understood that antibody binding to the peptide is still selective despite some degree of cross-reactivity.

As used herein, an antibody is defined in terms consistent with that recognized within the art: they are multi-subunit proteins produced by a mammalian organism in response to an antigen challenge. The antibodies of the present invention include polyclonal antibodies and monoclonal antibodies, as well as fragments of such antibodies, including, but not limited to, Fab or F(ab′)₂, and Fv fragments.

Many methods are known for generating and/or identifying antibodies to a given target peptide. Several such methods are described by Harlow, Antibodies, Cold Spring Harbor Press, (1989).

In general, to generate antibodies, an isolated peptide is used as an immunogen and is administered to a mammalian organism, such as a rat, rabbit or mouse. The full-length protein, an antigenic peptide fragment or a fusion protein can be used. Particularly important fragments are those covering functional domains, such as the domains identified in FIG. 2, and domain of sequence homology or divergence amongst the family, such as those that can readily be identified using protein alignment methods and as presented in the Figures.

Antibodies are preferably prepared from regions or discrete fragments of the kinase proteins. Antibodies can be prepared from any region of the peptide as described herein. However, preferred regions will include those involved in function/activity and/or kinase/binding partner interaction. FIG. 2 can be used to identify particularly important regions while sequence alignment can be used to identify conserved and unique sequence fragments.

An antigenic fragment will typically comprise at least 8 contiguous amino acid residues. The antigenic peptide can comprise, however, at least 10, 12, 14, 16 or more amino acid residues. Such fragments can be selected on a physical property, such as fragments correspond to regions that are located on the surface of the protein, e.g., hydrophilic regions or can be selected based on sequence uniqueness (see FIG. 2).

Detection on an antibody of the present invention can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S or ³H.

Antibody Uses

The antibodies can be used to isolate one of the proteins of the present invention by standard techniques, such as affinity chromatography or immunoprecipitation. The antibodies can facilitate the purification of the natural protein from cells and recombinantly produced protein expressed in host cells. In addition, such antibodies are useful to detect the presence of one of the proteins of the present invention in cells or tissues to determine the pattern of expression of the protein among various tissues in an organism and over the course of normal development. Experimental data as provided in FIG. 1. indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiated adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte. Further, such antibodies can be used to detect protein in situ, in vitro, or in a cell lysate or supernatant in order to evaluate the abundance and pattern of expression. Also, such antibodies can be used to assess abnormal tissue distribution or abnormal expression during development or progression of a biological condition. Antibody detection of circulating fragments of the full length protein can be used to identify turnover.

Further, the antibodies can be used to assess expression in disease states such as in active stages of the disease or in an individual with a predisposition toward disease related to the protein's function. When a disorder is caused by an inappropriate tissue distribution, developmental expression, level of expression of the protein, or expressed/processed form, the antibody can be prepared against the normal protein. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiated adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. If a disorder is characterized by a specific mutation in the protein, antibodies specific for this mutant protein can be used to assay for the presence of the specific mutant protein.

The antibodies can also be used to assess normal and aberrant subcellular localization of cells in the various tissues in an organism. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. The diagnostic uses can be applied, not only in genetic testing, but also in monitoring a treatment modality. Accordingly, where treatment is ultimately aimed at correcting expression level or the presence of aberrant sequence and aberrant tissue distribution or developmental expression, antibodies directed against the protein or relevant fragments can be used to monitor therapeutic efficacy.

Additionally, antibodies are useful in pharmacogenomic analysis. Thus, antibodies prepared against polymorphic proteins can be used to identify individuals that require modified treatment modalities. The antibodies are also useful as diagnostic tools as an immunological marker for aberrant protein analyzed by electrophoretic mobility, isoelectric point, tryptic peptide digest, and other physical assays known to those in the art.

The antibodies are also useful for tissue typing. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiated adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. Thus, where a specific protein has been correlated with expression in a specific tissue, antibodies that are specific for this protein can be used to identify a tissue type.

The antibodies are also useful for inhibiting protein function, for example, blocking the binding of the kinase peptide to a binding partner such as a substrate. These uses can also be applied in a therapeutic context in which treatment involves inhibiting the protein's function. An antibody can be used, for example, to block binding, thus modulating (agonizing or antagonizing) the peptides activity. Antibodies can be prepared against specific fragments containing sites required for function or against intact protein that is associated with a cell or cell membrane. See FIG. 2 for structural information relating to the proteins of the present invention.

The invention also encompasses kits for using antibodies to detect the presence of a protein in a biological sample. The kit can comprise antibodies such as a labeled or labelable antibody and a compound or agent for detecting protein in a biological sample; means for determining the amount of protein in the sample; means for comparing, the amount of protein in the sample with a standard; and instructions for use. Such a kit can be supplied to detect a single protein or epitope or can be configured to detect one of a multitude of epitopes, such as in an antibody detection array. Arrays are described in detail below for nuleic acid arrays and similar methods have been developed for antibody arrays.

Nucleic Acid Molecules

The present invention further provides isolated nucleic acid molecules that encode a kinase peptide or protein of the present invention (cDNA, transcript and genomic sequence). Such nucleic acid molecules will consist of, consist essentially of, or comprise a nucleotide sequence that encodes one of the kinase peptides of the present invention, an allelic variant thereof, or an ortholog or paralog thereof.

As used herein, an “isolated” nucleic acid molecule is one that is separated from other nucleic acid present in the natural source of the nucleic acid. Preferably, an “isolated” nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. However, there can be some flanking nucleotide sequences, for example up to about 5KB, 4KB, 3KB, 2KB, or 1KB or less, particularly contiguous peptide encoding sequences and peptide encoding sequences within the same gene but separated by introns in the genomic sequence. The important point is that the nucleic acid is isolated from remote and unimportant flanking sequences such that it can be subjected to the specific manipulations described herein such as recombinant expression, preparation of probes and primers, and other uses specific to the nucleic acid sequences.

Moreover, an “isolated” nucleic acid molecule, such as a transcript/cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized. However, the nucleic acid molecule can be fused to other coding or regulatory sequences and still be considered isolated.

For example, recombinant DNA molecules contained in a vector are considered isolated. Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the isolated DNA molecules of the present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.

Accordingly, the present invention provides nucleic acid molecules that consist of the nucleotide sequence shown in FIG. 1 or 3 (SEQ ID NO:1, transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleic acid molecule that encodes the protein provided in FIG. 2, SEQ ID NO:2. A nucleic acid molecule consists of a nucleotide sequence when the nucleotide sequence is the complete nucleotide sequence of the nucleic acid molecule.

The present invention further provides nucleic acid molecules that consist essentially of the nucleotide sequence shown in FIG. 1 or 3 (SEQ ID NO:1, transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleic acid molecule that encodes the protein provided in FIG. 2, SEQ ID NO:2. A nucleic acid molecule consists essentially of a nucleotide sequence when such a nucleotide sequence is present with only a few additional nucleic acid residues in the final nucleic acid molecule.

The present invention further provides nucleic acid molecules that comprise the nucleotide sequences shown in FIG. 1 or 3 (SEQ ID NO:1, transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleic acid molecule that encodes the protein provided in FIG. 2, SEQ ID NO:2. A nucleic acid molecule comprises a nucleotide sequence when the nucleotide sequence is at least part of the final nucleotide sequence of the nucleic acid molecule. In such a fashion, the nucleic acid molecule can be only the nucleotide sequence or have additional nucleic acid residues, such as nucleic acid residues that are naturally associated with it or heterologous nucleotide sequences. Such a nucleic acid molecule can have a few additional nucleotides or can comprises several hundred or more additional nucleotides. A brief description of how various types of these nucleic acid molecules can be readily made/isolated is provided below.

In FIGS. 1 and 3, both coding and non-coding sequences are provided. Because of the source of the present invention, humans genomic sequence (FIG. 3) and cDNA/transcript sequences (FIG. 1), the nucleic acid molecules in the Figures will contain genomic intronic sequences, 5′ and 3′ non-coding sequences, gene regulatory regions and non-coding intergenic sequences. In general such sequence features are either noted in FIGS. 1 and 3 or can readily be identified using computational tools known in the art. As discussed below, some of the non-coding regions, particularly gene regulatory elements such as promoters, are useful for a variety of purposes, e.g. control of heterologous gene expression, target for identifying gene activity modulating compounds, and are particularly claimed as fragments of the genomic sequence provided herein.

The isolated nucleic acid molecules can encode the mature protein plus additional amino or carboxyl-terminal amino acids, or amino acids interior to the mature peptide (when the mature form has more than one peptide chain, for instance). Such sequences may play a role in processing of a protein from precursor to a mature form, facilitate protein trafficking, prolong or shorten protein half-life or facilitate manipulation of a protein for assay or production, among other things. As generally is the case in situ, the additional amino acids may be processed away from the mature protein by cellular enzymes.

As mentioned above, the isolated nucleic acid molecules include, but are not limited to, the sequence encoding the kinase peptide alone, the sequence encoding the mature peptide and additional coding sequences, such as a leader or secretory sequence (e.g., a pre-pro or pro-protein sequence), the sequence encoding the mature peptide, with or without the additional coding sequences, plus additional non-coding sequences, for example introns and non-coding 5′ and 3′ sequences such as transcribed but non-translated sequences that play a role in transcription, mRNA processing (including splicing and polyadenylation signals), ribosome binding and stability of mRNA. In addition, the nucleic acid molecule may be fused to a marker sequence encoding, for example, a peptide that facilitates purification.

Isolated nucleic acid molecules can be in the form of RNA, such as mRNA, or in the form DNA, including cDNA and genomic DNA obtained by cloning or produced by chemical synthetic techniques or by a combination thereof. The nucleic acid, especially DNA, can be double-stranded or single-stranded. Single-stranded nucleic acid can be the coding strand (sense strand) or the non-coding strand (anti-sense strand).

The invention further provides nucleic acid molecules that encode fragments of the peptides of the present invention as well as nucleic acid molecules that encode obvious variants of the kinase proteins of the present invention that are described above. Such nucleic acid molecules may be naturally occurring, such as allelic variants (same locus), paralogs (different locus), and orthologs (different organism), or may be constructed by recombinant DNA methods or by chemical synthesis. Such non-naturally occurring variants may be made by mutagenesis techniques, including those applied to nucleic acid molecules, cells, or organisms. Accordingly, as discussed above, the variants can contain nucleotide substitutions, deletions, inversions and insertions. Variation can occur in either or both the coding and non-coding regions. The variations can produce both conservative and non-conservative amino acid substitutions.

The present invention further provides non-coding fragments of the nucleic acid molecules provided in FIGS. 1 and 3. Preferred non-coding fragments include, but are not limited to, promoter sequences, enhancer sequences, gene modulating sequences and gene termination sequences. Such fragments are useful in controlling heterologous gene expression and in developing screens to identify gene-modulating agents. A promoter can readily be identified as being 5′ to the ATG start site in the genomic sequence provided in FIG. 3.

A fragment comprises a contiguous nucleotide sequence greater than 12 or more nucleotides. Further, a fragment could at least 30, 40, 50, 100, 250 or 500 nucleotides in length. The length of the fragment will be based on its intended use. For example, the fragment can encode epitope bearing regions of the peptide, or can be useful as DNA probes and primers. Such fragments can be isolated using the known nucleotide sequence to synthesize an oligonucleotide probe. A labeled probe can then be used to screen a cDNA library, genomic DNA library, or mRNA to isolate nucleic acid corresponding to the coding region. Further, primers can be used in PCR reactions to clone specific regions of gene.

A probe/primer typically comprises substantially a purified oligonucleotide or oligonucleotide pair. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, 20, 25, 40, 50 or more consecutive nucleotides.

Orthologs, homologs, and allelic variants can be identified using methods well known in the art. As described in the Peptide Section, these variants comprise a nucleotide sequence encoding a peptide that is typically 60-70%, 70-80%, 80-90%, and more typically at least about 90-95% or more homologous to the nucleotide sequence shown in the Figure sheets or a fragment of this sequence. Such nucleic acid molecules can readily be identified as being able to hybridize under moderate to stringent conditions, to the nucleotide sequence shown in the Figure sheets or a fragment of the sequence. Allelic variants can readily be determined by genetic locus of the encoding gene. As indicated by the data presented in FIG. 3, the map position was determined to be on chromosome 5 by ePCR.

FIG. 3 provides information on SNPs that have been found in the gene encoding the transporter protein of the present invention. SNPs were identified at 10 different nucleotide positions in introns and regions 5′ and 3′ of the ORF. Such SNPs in introns and outside the ORF may affect control/regulatory elements.

As used herein, the term “hybridizes under stringent conditions” is intended to describe conditions for hybridization and washing under which nucleotide sequences encoding a peptide at least 60-70% homologous to each other typically remain hybridized to each other. The conditions can be such that sequences at least about 60%, at least about 70%, or at least about 80% or more homologous to each other typically remain hybridized to each other. Such stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. One example of stringent hybridization conditions are hybridization in 6×sodium chloride/sodium citrate (SSC) at about 45C, followed by one or more washes in 0.2×SSC, 0.1% SDS at 50-65C. Examples of moderate to low stringency hybridization conditions are well known in the art.

Nucleic Acid Molecule Uses

The nucleic acid molecules of the present invention are useful for probes, primers, chemical intermediates, and in biological assays. The nucleic acid molecules are useful as a hybridization probe for messenger RNA, transcript/cDNA and genomic DNA to isolate full-length cDNA and genomic clones encoding the peptide described in FIG. 2 and to isolate cDNA and genomic clones that correspond to variants (alleles, orthologs, etc.) producing the same or related peptides shown in FIG. 2. As illustrated in FIG. 3, SNPs, including insertion/deletion variants (“indels”), were identified at 10 different nucleotide positions.

The probe can correspond to any sequence along the entire length of the nucleic acid molecules provided in the Figures. Accordingly, it could be derived from 5′ noncoding regions, the coding region, and 3′ noncoding regions. However, as discussed, fragments are not to be construed as encompassing fragments disclosed prior to the present invention.

The nucleic acid molecules are also useful as primers for PCR to amplify any given region of a nucleic acid molecule and are useful to synthesize antisense molecules of desired length and sequence.

The nucleic acid molecules are also useful for constructing recombinant vectors. Such vectors include expression vectors that express a portion of, or all of, the peptide sequences. Vectors also include insertion vectors, used to integrate into another nucleic acid molecule sequence, such as into the cellular genome, to alter in situ expression of a gene and/or gene product. For example, an endogenous coding sequence can be replaced via homologous recombination with all or part of the coding region containing one or more specifically introduced mutations.

The nucleic acid molecules are also useful for expressing antigenic portions of the proteins.

The nucleic acid molecules are also useful as probes for determining the chromosomal positions of the nucleic acid molecules by means of in situ hybridization methods. As indicated by the data presented in FIG. 3, the map position was determined to be on chromosome 5 by ePCR.

The nucleic acid molecules are also useful in making vectors containing the gene regulatory regions of the nucleic acid molecules of the present invention.

The nucleic acid molecules are also useful for designing ribozymes corresponding to all, or a part, of the mRNA produced from the nucleic acid molecules described herein.

The nucleic acid molecules are also useful for making vectors that express part, or all, of the peptides.

The nucleic acid molecules are also useful for constructing host cells expressing a part, or all, of the nucleic acid molecules and peptides.

The nucleic acid molecules are also useful for constructing transgenic animals expressing all, or a part, of the nucleic acid molecules and peptides.

The nucleic acid molecules are also useful as hybridization probes for determining the presence, level, form and distribution of nucleic acid expression. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte. Accordingly, the probes can be used to detect the presence of, or to determine levels of, a specific nucleic acid molecule in cells, tissues, and in organisms. The nucleic acid whose level is determined can be DNA or RNA. Accordingly, probes corresponding to the peptides described herein can be used to assess expression and/or gene copy number in a given cell, tissue, or organism. These uses are relevant for diagnosis of disorders involving an increase or decrease in kinase protein expression relative to normal results.

In vitro techniques for detection of mRNA include Northern hybridizations and in situ hybridizations. In vitro techniques for detecting DNA includes Southern hybridizations and in situ hybridization.

Probes can be used as a part of a diagnostic test kit for identifying cells or tissues that express a kinase protein, such as by measuring a level of a kinase-encoding nucleic acid in a sample of cells from a subject e.g., mRNA or genomic DNA, or determining if a kinase gene has been mutated. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte.

Nucleic acid expression assays are useful for drug screening to identify compounds that modulate kinase nucleic acid expression.

The invention thus provides a method for identifying a compound that can be used to treat a disorder associated with nucleic acid expression of the kinase gene, particularly biological and pathological processes that are mediated by the kinase in cells and tissues that express it. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte. The method typically includes assaying the ability of the compound to modulate the expression of the kinase nucleic acid and thus identifying a compound that can be used to treat a disorder characterized by undesired kinase nucleic acid expression. The assays can be performed in cell-based and cell-free systems. Cell-based assays include cells naturally expressing the kinase nucleic acid or recombinant cells genetically engineered to express specific nucleic acid sequences.

The assay for kinase nucleic acid expression can involve direct assay of nucleic acid levels, such as mRNA levels, or on collateral compounds involved in the signal pathway. Further, the expression of genes that are up- or down-regulated in response to the kinase protein signal pathway can also be assayed. In this embodiment the regulatory regions of these genes can be operably linked to a reporter gene such as luciferase.

Thus, modulators of kinase gene expression can be identified in a method wherein a cell is contacted with a candidate compound and the expression of mRNA determined. The level of expression of kinase mRNA in the presence of the candidate compound is compared to the level of expression of kinase mRNA in the absence of the candidate compound. The candidate compound can then be identified as a modulator of nucleic acid expression based on this comparison and be used, for example to treat a disorder characterized by aberrant nucleic acid expression. When expression of mRNA is statistically significantly greater in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of nucleic acid expression. When nucleic acid expression is statistically significantly less in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of nucleic acid expression.

The invention further provides methods of treatment, with the nucleic acid as a target, using a compound identified through drug screening as a gene modulator to modulate kinase nucleic acid expression in cells and tissues that express the kinase. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte. Modulation includes both up-regulation (i.e. activation or agonization) or down-regulation (suppression or antagonization) or nucleic acid expression.

Alternatively, a modulator for kinase nucleic acid expression can be a small molecule or drug identified using the screening assays described herein as long as the drug or small molecule inhibits the kinase nucleic acid expression in the cells and tissues that express the protein. Experimental data as provided in FIG. 1 indicates expression in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis, myeloid cell as well as leukocyte.

The nucleic acid molecules are also useful for monitoring the effectiveness of modulating compounds on the expression or activity of the kinase gene in clinical trials or in a treatment regimen. Thus, the gene expression pattern can serve as a barometer for the continuing effectiveness of treatment with the compound, particularly with compounds to which a patient can develop resistance. The gene expression pattern can also serve as a marker indicative of a physiological response of the affected cells to the compound. Accordingly, such monitoring would allow either increased administration of the compound or the administration of alternative compounds to which the patient has not become resistant. Similarly, if the level of nucleic acid expression falls below a desirable level, administration of the compound could be commensurately decreased.

The nucleic acid molecules are also useful in diagnostic assays for qualitative changes in kinase nucleic acid expression, and particularly in qualitative changes that lead to pathology. The nucleic acid molecules can be used to detect mutations in kinase genes and gene expression products such as mRNA. The nucleic acid molecules can be used as hybridization probes to detect naturally occurring genetic mutations in the kinase gene and thereby to determine whether a subject with the mutation is at risk for a disorder caused by the mutation. Mutations include deletion, addition, or substitution of one or more nucleotides in the gene, chromosomal rearrangement, such as inversion or transposition, modification of genomic DNA, such as aberrant methylation patterns or changes in gene copy number, such as amplification. Detection of a mutated form of the kinase gene associated with a dysfunction provides a diagnostic tool for an active disease or susceptibility to disease when the disease results from overexpression, underexpression, or altered expression of a kinase protein.

Individuals carrying mutations in the kinase gene can be detected at the nucleic acid level by a variety of techniques. FIG. 3 provides information on SNPs that have been found in the gene encoding the transporter protein of the present invention. SNPs were identified at 10 different nucleotide positions in introns and regions 5′ and 3′ of the ORF. Such SNPs in introns and outside the ORF may affect control/regulatory elements. As indicated by the data presented in FIG. 3, the map position was determined to be on chromosome 5 by ePCR. Genomic DNA can be analyzed directly or can be amplified by using PCR prior to analysis. RNA or cDNA can be used in the same way. In some uses, detection of the mutation involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g. U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al., Science 241:1077-1080 (1988); and Nakazawa et al., PNAS 91:360-364 (1994)), the latter of which can be particularly useful for detecting point mutations in the gene (see Abravaya et al., Nucleic Acids Res. 23:675-682 (1995)). This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a gene under conditions such that hybridization and amplification of the gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. Deletions and insertions can be detected by a change in size of the amplified product compared to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to normal RNA or antisense DNA sequences.

Alternatively, mutations in a kinase gene can be directly identified, for example, by alterations in restriction enzyme digestion patterns determined by gel electrophoresis.

Further, sequence-specific ribozymes (U.S. Pat. No. 5,498,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site. Perfectly matched sequences can be distinguished from mismatched sequences by nuclease cleavage digestion assays or by differences in melting temperature.

Sequence changes at specific locations can also be assessed by nuclease protection assays such as RNase and S1 protection or the chemical cleavage method. Furthermore, sequence differences between a mutant kinase gene and a wild-type gene can be determined by direct DNA sequencing. A variety of automated sequencing procedures can be utilized when performing the diagnostic assays (Naeve, C. W., (1995) Biotechniques 19:448), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen et al., Adv. Chromatogr. 36:127-162 (1996); and Griffin et al., Appl. Biochem. Biotechnol. 38:147-159 (1993)).

Other methods for detecting mutations in the gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA duplexes (Myers et al., Science 230:1242 (1985)); Cotton et al., PNAS 85:4397 (1988); Saleeba et al., Meth. Enzymol. 217:286-295 (1992)), electrophoretic mobility of mutant and wild type nucleic acid is compared (Orita et al., PNAS 86:2766 (1989); Cotton et al., Mutat. Res. 285:125-144 (1993); and Hayashi et al., Genet. Anal. Tech. Appl. 9:73-79 (1992)), and movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (Myers et al., Nature 313:495 (1985)). Examples of other techniques for detecting point mutations include selective oligonucleotide hybridization, selective amplification, and selective primer extension.

The nucleic acid molecules are also useful for testing an individual for a genotype that while not necessarily causing the disease, nevertheless affects the treatment modality. Thus, the nucleic acid molecules can be used to study the relationship between an individual's genotype and the individual's response to a compound used for treatment (pharmacogenomic relationship). Accordingly, the nucleic acid molecules described herein can be used to assess the mutation content of the kinase gene in an individual in order to select an appropriate compound or dosage regimen for treatment. FIG. 3 provides information on SNPs that have been found in the gene encoding the transporter protein of the present invention. SNPs were identified at 10 different nucleotide positions in introns and regions 5′ and 3′ of the ORF. Such SNPs in introns and outside the ORF may affect control/regulatory elements.

Thus nucleic acid molecules displaying genetic variations that affect treatment provide a diagnostic target that can be used to tailor treatment in an individual. Accordingly, the production of recombinant cells and animals containing these polymorphisms allow effective clinical design of treatment compounds and dosage regimens.

The nucleic acid molecules are thus useful as antisense constructs to control kinase gene expression in cells, tissues, and organisms. A DNA antisense nucleic acid molecule is designed to be complementary to a region of the gene involved in transcription, preventing transcription and hence production of kinase protein. An antisense RNA or DNA nucleic acid molecule would hybridize to the mRNA and thus block translation of mRNA into kinase protein.

Alternatively, a class of antisense molecules can be used to inactivate mRNA in order to decrease expression of kinase nucleic acid. Accordingly, these molecules can treat a disorder characterized by abnormal or undesired kinase nucleic acid expression. This technique involves cleavage by means of ribozymes containing nucleotide sequences complementary to one or more regions in the mRNA that attenuate the ability of the mRNA to be translated. Possible regions include coding regions and particularly coding regions corresponding to the catalytic and other functional activities of the kinase protein, such as substrate binding.

The nucleic acid molecules also provide vectors for gene therapy in patients containing cells that are aberrant in kinase gene expression. Thus, recombinant cells, which include the patient's cells that have been engineered ex vivo and returned to the patient, are introduced into an individual where the cells produce the desired kinase protein to treat the individual.

The invention also encompasses kits for detecting the presence of a kinase nucleic acid in a biological sample. Experimental data as provided in FIG. 1 indicates that kinase proteins of the present invention are expressed in the bone osteosarcoma cell line, breast, uterus leiomyosarcoma, fetal heart, infant brain, colon-juvenile granulose tumor, colon-moderately differentiatd adenocarcinoma, bone marrow hematopoietic stem cells, pooled human melanocyte, fetal heart, and pregnant uterus, normal nerve, leukopheresis,myeloid cell as well as leukocyte by a virtual northern blot. In addition, PCR-based tissue screening panel indicates expression in leukocyte. For example, the kit can comprise reagents such as a labeled or labelable nucleic acid or agent capable of detecting kinase nucleic acid in a biological sample; means for determining the amount of kinase nucleic acid in the sample; and means for comparing the amount of kinase nucleic acid in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect kinase protein mRNA or DNA.

Nucleic Acid Arrays

The present invention further provides nucleic acid detection kits, such as arrays or microarrays of nucleic acid molecules that are based on the sequence information provided in FIGS. 1 and 3 (SEQ ID NOS:1 and 3).

As used herein “Arrays” or “Microarrays” refers to an array of distinct polynucleotides or oligonucleotides synthesized on a substrate, such as paper, nylon or other type of membrane, filter, chip, glass slide, or any other suitable solid support. In one embodiment, the microarray is prepared and used according to the methods described in U.S. Pat. No. 5,837,832, Chee et al., PCT application WO95/11995 (Chee et al.), Lockhart, D. J. et al. (1996; Nat. Biotech. 14: 1675-1680) and Schena, M. et al. (1996; Proc. Natl. Acad. Sci. 93: 10614-10619), all of which are incorporated herein in their entirety by reference. In other embodiments, such arrays are produced by the methods described by Brown et al., U.S. Pat. No. 5,807,522.

The microarray or detection kit is preferably composed of a large number of unique, single-stranded nucleic acid sequences, usually either synthetic antisense oligonucleotides or fragments of cDNAs, fixed to a solid support. The oligonucleotides are preferably about 6-60 nucleotides in length, more preferably 15-30 nucleotides in length, and most preferably about 20-25 nucleotides in length. For a certain type of microarray or detection kit, it may be preferable to use oligonucleotides that are only 7-20 nucleotides in length. The microarray or detection kit may contain oligonucleotides that cover the known 5′, or 3′, sequence, sequential oligonucleotides which cover the full length sequence; or unique oligonucleotides selected from particular areas along the length of the sequence. Polynucleotides used in the microarray or detection kit may be oligonucleotides that are specific to a gene or genes of interest.

In order to produce oligonucleotides to a known sequence for a microarray or detection kit, the gene(s) of interest (or an ORF identified from the contigs of the present invention) is typically examined using a computer algorithm which starts at the 5′ or at the 3′ end of the nucleotide sequence. Typical algorithms will then identify oligomers of defined length that are unique to the gene, have a GC content within a range suitable for hybridization, and lack predicted secondary structure that may interfere with hybridization. In certain situations it may be appropriate to use pairs of oligonucleotides on a microarray or detection kit. The “pairs” will be identical, except for one nucleotide that preferably is located in the center of the sequence. The second oligonucleotide in the pair (mismatched by one) serves as a control. The number of oligonucleotide pairs may range from two to one million. The oligomers are synthesized at designated areas on a substrate using a light-directed chemical process. The substrate may be paper, nylon or other type of membrane, filter, chip, glass slide or any other suitable solid support.

In another aspect, an oligonucleotide may be synthesized on the surface of the substrate by using a chemical coupling procedure and an ink jet application apparatus, as described in PCT application WO95/251116 (Baldeschweiler et al.) which is incorporated herein in its entirety by reference. In another aspect, a “gridded” array analogous to a dot (or slot) blot may be used to arrange and link cDNA fragments or oligonucleotides to the surface of a substrate using a vacuum system, thermal, UV, mechanical or chemical bonding procedures. An array, such as those described above, may be produced by hand or by using available devices (slot blot or dot blot apparatus), materials (any suitable solid support), and machines (including robotic instruments), and may contain 8, 24, 96, 384, 1536, 6144 or more oligonucleotides, or any other number between two and one million which lends itself to the efficient use of commercially available instrumentation.

In order to conduct sample analysis using a microarray or detection kit, the RNA or DNA from a biological sample is made into hybridization probes. The mRNA is isolated, and cDNA is produced and used as a template to make antisense RNA (aRNA). The aRNA is amplified in the presence of fluorescent nucleotides, and labeled probes are incubated with the microarray or detection kit so that the probe sequences hybridize to complementary oligonucleotides of the microarray or detection kit. Incubation conditions are adjusted so that hybridization occurs with precise complementary matches or with various degrees of less complementarity. After removal of nonhybridized probes, a scanner is used to determine the levels and patterns of fluorescence. The scanned images are examined to determine degree of complementarity and the relative abundance of each oligonucleotide sequence on the microarray or detection kit. The biological samples may be obtained from any bodily fluids (such as blood, urine, saliva, phlegm, gastric juices, etc.), cultured cells, biopsies, or other tissue preparations. A detection system may be used to measure the absence, presence, and amount of hybridization for all of the distinct sequences simultaneously. This data may be used for large-scale correlation studies on the sequences, expression patterns, mutations, variants, or polymorphisms among samples.

Using such arrays, the present invention provides methods to identify the expression of the kinase proteins/peptides of the present invention. In detail, such methods comprise incubating a test sample with one or more nucleic acid molecules and assaying for binding of the nucleic acid molecule with components within the test sample. Such assays will typically involve arrays comprising many genes, at least one of which is a gene of the present invention and or alleles of the kinase gene of the present invention. FIG. 3 provides information on SNPs that have been found in the gene encoding the transporter protein of the present invention. SNPs were identified at 10 different nucleotide positions in introns and regions 5′ and 3′ of the ORF. Such SNPs in introns and outside the ORF may affect control/regulatory elements.

Conditions for incubating a nucleic acid molecule with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the nucleic acid molecule used in the assay. One skilled in the art will recognize that any one of the commonly available hybridization, amplification or array assay formats can readily be adapted to employ the novel fragments of the Human genome disclosed herein. Examples of such assays can be found in Chard, T, An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques in Immunocytochemistry, Academic Press, Orlando, Fla. Vol. 1(1 982), Vol.2 (1983), Vol.3 (1985); Tijssen, P., Practice and Theory of Enzyme Immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985).

The test samples of the present invention include cells, protein or membrane extracts of cells. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing nucleic acid extracts or of cells are well known in the art and can be readily be adapted in order to obtain a sample that is compatible with the system utilized.

In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention.

Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the nucleic acid molecules that can bind to a fragment of the Human genome disclosed herein; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound nucleic acid.

In detail, a compartmentalized kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers, strips of plastic, glass or paper, or arraying material such as silica. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the nucleic acid probe, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound probe. One skilled in the art will readily recognize that the previously unidentified kinase gene of the present invention can be routinely identified using the sequence information disclosed herein can be readily incorporated into one of the established kit formats which are well known in the art, particularly expression arrays.

Vectors/host Cells

The invention also provides vectors containing the nucleic acid molecules described herein. The term “vector” refers to a vehicle, preferably a nucleic acid molecule, which can transport the nucleic acid molecules. When the vector is a nucleic acid molecule, the nucleic acid molecules are covalently linked to the vector nucleic acid. With this aspect of the invention, the vector includes a plasmid, single or double stranded phage, a single or double stranded RNA or DNA viral vector, or artificial chromosome, such as a BAC, PAC, YAC, OR MAC.

A vector can be maintained in the host cell as an extrachromosomal element where it replicates and produces additional copies of the nucleic acid molecules. Alternatively, the vector may integrate into the host cell genome and produce additional copies of the nucleic acid molecules when the host cell replicates.

The invention provides vectors for the maintenance (cloning vectors) or vectors for expression (expression vectors) of the nucleic acid molecules. The vectors can function in prokaryotic or eukaryotic cells or in both (shuttle vectors).

Expression vectors contain cis-acting regulatory regions that are operably linked in the vector to the nucleic acid molecules such that transcription of the nucleic acid molecules is allowed in a host cell. The nucleic acid molecules can be introduced into the host cell with a separate nucleic acid molecule capable of affecting transcription. Thus, the second nucleic acid molecule may provide a trans-acting factor interacting with the cis-regulatory control region to allow transcription of the nucleic acid molecules from the vector. Alternatively, a trans-acting factor may be supplied by the host cell. Finally, a trans-acting factor can be produced from the vector itself. It is understood, however, that in some embodiments, transcription and/or translation of the nucleic acid molecules can occur in a cell-free system.

The regulatory sequence to which the nucleic acid molecules described herein can be operably linked include promoters for directing mRNA transcription. These include, but are not limited to, the left promoter from bacteriophage λ, the lac, TRP, and TAC promoters from E. coli, the early and late promoters from SV40, the CMV immediate early promoter, the adenovirus early and late promoters, and retrovirus long-terminal repeats.

In addition to control regions that promote transcription, expression vectors may also include regions that modulate transcription, such as repressor binding sites and enhancers. Examples include the SV40 enhancer, the cytomegalovirus immediate early enhancer, polyoma enhancer, adenovirus enhancers, and retrovirus LTR enhancers.

In addition to containing sites for transcription initiation and control, expression vectors can also contain sequences necessary for transcription termination and, in the transcribed region a ribosome binding site for translation. Other regulatory control elements for expression include initiation and termination codons as well as polyadenylation signals. The person of ordinary skill in the art would be aware of the numerous regulatory sequences that are useful in expression vectors. Such regulatory sequences are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual. 2nd. ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., (1989).

A variety of expression vectors can be used to express a nucleic acid molecule. Such vectors include chromosomal, episomal, and virus-derived vectors, for example vectors derived from bacterial plasmids, from bacteriophage, from yeast episomes, from yeast chromosomal elements, including yeast artificial chromosomes, from viruses such as baculoviruses, papovaviruses such as SV40, Vaccinia viruses, adenoviruses, poxviruses, pseudorabies viruses, and retroviruses. Vectors may also be derived from combinations of these sources such as those derived from plasmid and bacteriophage genetic elements, e.g. cosmids and phagemids. Appropriate cloning and expression vectors for prokaryotic and eukaryotic hosts are described in Sambrook et al., Molecular Cloning: A Laboratory Manual. 2nd. ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., (1989).

The regulatory sequence may provide constitutive expression in one or more host cells (i.e. tissue specific) or may provide for inducible expression in one or more cell types such as by temperature, nutrient additive, or exogenous factor such as a hormone or other ligand. A variety of vectors providing for constitutive and inducible expression in prokaryotic and eukaryotic hosts are well known to those of ordinary skill in the art.

The nucleic acid molecules can be inserted into the vector nucleic acid by well-known methodology. Generally, the DNA sequence that will ultimately be expressed is joined to an expression vector by cleaving the DNA sequence and the expression vector with one or more restriction enzymes and then ligating the fragments together. Procedures for restriction enzyme digestion and ligation are well known to those of ordinary skill in the art.

The vector containing the appropriate nucleic acid molecule can be introduced into an appropriate host cell for propagation or expression using well-known techniques. Bacterial cells include, but are not limited to, E. coli, Streptomyces, and Salmonella typhimurium. Eukaryotic cells include, but are not limited to, yeast, insect cells such as Drosophila, animal cells such as COS and CHO cells, and plant cells.

As described herein, it may be desirable to express the peptide as a fusion protein. Accordingly, the invention provides fusion vectors that allow for the production of the peptides. Fusion vectors can increase the expression of a recombinant protein, increase the solubility of the recombinant protein, and aid in the purification of the protein by acting for example as a ligand for affinity purification. A proteolytic cleavage site may be introduced at the junction of the fusion moiety so that the desired peptide can ultimately be separated from the fusion moiety. Proteolytic enzymes include, but are not limited to, factor Xa, thrombin, and enterokinase. Typical fusion expression vectors include pGEX (Smith et al., Gene 67:31-40 (1988)), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., Gene 69:301-315 (1988)) and pET 1d (Studier et al., Gene Expression Technology: Methods in Enzymology 185:60-89 (1990)).

Recombinant protein expression can be maximized in host bacteria by providing a genetic background wherein the host cell has an impaired capacity to proteolytically cleave the recombinant protein. (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128). Alternatively, the sequence of the nucleic acid molecule of interest can be altered to provide preferential codon usage for a specific host cell, for example E. coli. (Wada et al., Nucleic Acids Res. 20:2111-2118 (1992)).

The nucleic acid molecules can also be expressed by expression vectors that are operative in yeast. Examples of vectors for expression in yeast e.g., S. cerevisiae include pYepSec1 (Baldari, et al., EMBO J. 6:229-234 (1987)), pMFa (Kurjan et al., Cell 30:933-943(1982)), pJRY88 (Schultz et al., Gene 54:113-123 (1987)), and pYES2 (Invitrogen Corporation, San Diego, Calif.).

The nucleic acid molecules can also be expressed in insect cells using, for example, baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf9 cells) include the pAc series (Smith et al., Mol. Cell Biol. 3:2156-2165 (1983)) and the pVL series (Lucklow et al., Virology 170:31-39 (1989)).

In certain embodiments of the invention, the nucleic acid molecules described herein are expressed in mammalian cells using mammalian expression vectors. Examples of mammalian expression vectors include pCDM8 (Seed, B. Nature 329:840(1987)) and pMT2PC (Kaufman et al., EMBO J. 6:187-195 (1987)).

The expression vectors listed herein are provided by way of example only of the well-known vectors available to those of ordinary skill in the art that would be useful to express the nucleic acid molecules. The person of ordinary skill in the art would be aware of other vectors suitable for maintenance propagation: or expression of the nucleic acid molecules described herein. These are found for example in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

The invention also encompasses vectors in which the nucleic acid sequences described herein are cloned into the vector in reverse orientation, but operably linked to a regulatory sequence that permits transcription of antisense RNA. Thus, an antisense transcript can be produced to all, or to a portion, of the nucleic acid molecule sequences described herein, including both coding and non-coding regions. Expression of this antisense RNA is subject to each of the parameters described above in relation to expression of the sense RNA (regulatory sequences, constitutive or inducible expression, tissue-specific expression).

The invention also relates to recombinant host cells containing the vectors described herein. Host cells therefore include prokaryotic cells, lower eukaryotic cells such as yeast, other eukaryotic cells such as insect cells, and higher eukaryotic cells such as mammalian cells.

The recombinant host cells are prepared by introducing the vector constructs described herein into the cells by techniques readily available to the person of ordinary skill in the art. These include, but are not limited to, calcium phosphate transfection, DEAE-dextran-mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, lipofection, and other techniques such as those found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989).

Host cells can contain more than one vector. Thus, different nucleotide sequences can be introduced on different vectors of the same cell. Similarly, the nucleic acid molecules can be introduced either alone or with other nucleic acid molecules that are not related to the nucleic acid molecules such as those providing transacting factors for expression vectors. When more than one vector is introduced into a cell, the vectors can be introduced independently, co-introduced or joined to the nucleic acid molecule vector.

In the case of bacteriophage and viral vectors, these can be introduced into cells as packaged or encapsulated virus by standard procedures for infection and transduction. Viral vectors can be replication-competent or replication-defective. In the case in which viral replication is defective, replication will occur in host cells providing functions that complement the defects.

Vectors generally include selectable markers that enable the selection of the subpopulation of cells that contain the recombinant vector constructs. The marker can be contained in the same vector that contains the nucleic acid molecules described herein or may be on a separate vector. Markers include tetracycline or ampicillin-resistance genes for prokaryotic host cells and dihydrofolate reductase or neomycin resistance for eukaryotic host cells. However, any marker that provides selection for a phenotypic trait will be effective.

While the mature proteins can be produced in bacteria, yeast, mammalian cells, and other cells under the control of the appropriate regulatory sequences, cell-free transcription and translation systems can also be used to produce these proteins using RNA derived from the DNA constructs described herein.

Where secretion of the peptide is desired, which is difficult to achieve with multi-transmembrane domain containing proteins such as kinases, appropriate secretion signals are incorporated into the vector. The signal sequence can be endogenous to the peptides or heterologous to these peptides.

Where the peptide is not secreted into the medium, which is typically the case with kinases, the protein can be isolated from the host cell by standard disruption procedures, including freeze thaw, sonication, mechanical disruption, use of lysing agents and the like. The peptide can then be recovered and purified by well-known purification methods including ammonium sulfate precipitation, acid extraction, anion or cationic exchange chromatography, phosphocellulose chromatography, hydrophobic-interaction chromatography, affinity chromatography, hydroxylapatite chromatography, lectin chromatography, or high performance liquid chromatography.

It is also understood that depending upon the host cell in recombinant production of the peptides described herein, the peptides can have various glycosylation patterns, depending upon the cell, or maybe non-glycosylated as when produced in bacteria. In addition, the peptides may include an initial modified methionine in some cases as a result of a host-mediated process.

Uses of Vectors and Host Cells

The recombinant host cells expressing the peptides described herein have a variety of uses. First, the cells are useful for producing a kinase protein or peptide that can be further purified to produce desired amounts of kinase protein or fragments. Thus, host cells containing expression vectors are useful for peptide production.

Host cells are also useful for conducting cell-based assays involving the kinase protein or kinase protein fragments, such as those described above as well as other formats known in the art. Thus, a recombinant host cell expressing a native kinase protein is useful for assaying compounds that stimulate or inhibit kinase protein function.

Host cells are also useful for identifying kinase protein mutants in which these functions are affected. If the mutants naturally occur and give rise to a pathology, host cells containing the mutations are useful to assay compounds that have a desired effect on the mutant kinase protein (for example, stimulating or inhibiting function) which may not be indicated by their effect on the native kinase protein.

Genetically engineered host cells can be further used to produce non-human transgenic animals. A transgenic animal is preferably a mammal, for example a rodent, such as a rat or mouse, in which one or more of the cells of the animal include a transgene. A transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal in one or more cell types or tissues of the transgenic animal. These animals are useful for studying the function of a kinase protein and identifying and evaluating modulators of kinase protein activity. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, and amphibians.

A transgenic animal can be produced by introducing nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal. Any of the kinase protein nucleotide sequences can be introduced as a transgene into the genome of a non-human animal, such as a mouse.

Any of the regulatory or other sequences useful in expression vectors can form part of the transgenic sequence. This includes intronic sequences and polyadenylation signals, if not already included. A tissue-specific regulatory sequence(s) can be operably linked to the transgene to direct expression of the kinase protein to particular cells.

Methods for generating transgenic animals via embryo manipulation and microinjection, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009, both by Leder et al., U.S. Pat. No. 4,873,191 by Wagner et al. and in Hogan, B., Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986). Similar methods are used for production of other transgenic animals. A transgenic founder animal can be identified based upon the presence of the transgene in its genome and/or expression of transgenic mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene can further be bred to other transgenic animals carrying other transgenes. A transgenic animal also includes animals in which the entire animal or tissues in the animal have been produced using the homologously recombinant host cells described herein.

In another embodiment, transgenic non-human animals can be produced which contain selected systems that allow for regulated expression of the transgene. One example of such a system is the cre/loxP recombinase system of bacteriophage P1. For a description of the cre/loxP recombinase system, see, e.g., Lakso et al. PNAS 89:6232-6236 (1992). Another example of a recombinase system is the FLP recombinase system of S. cerevisiae (O'Gorman et al. Science 251:1351-1355 (1991). If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein is required. Such animals can be provided through the construction of “double” transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.

Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, I. et al. Nature 385:810-813. (1997) and PCT International Publication Nos. WO 97/07668 and WO 97/07669. In brief, a cell, e.g., a somatic cell, from the transgenic animal can be isolated and induced to exit the growth cycle and enter G_(o) phase. The quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated. The reconstructed oocyte is then cultured such that it develops to morula or blastocyst and then transferred to pseudopregnant female foster animal. The offspring born of this female foster animal will be a clone of the animal from which the cell, e.g., the somatic cell, is isolated.

Transgenic animals containing recombinant cells that express the peptides described herein are useful to conduct the assays described herein in an in vivo context. Accordingly, the various physiological factors that are present in vivo and that could effect substrate binding, kinase protein activation, and signal transduction, may not be evident from in vitro cell-free or cell-based assays. Accordingly, it is useful to provide non-human transgenic animals to assay in vivo kinase protein function, including substrate interaction, the effect of specific mutant kinase proteins on kinase protein function and substrate interaction, and the effect of chimeric kinase proteins. It is also possible to assess the effect of null mutations, that is, mutations that substantially or completely eliminate one or more kinase protein functions.

All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims.

                   #             SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 5 <210> SEQ ID NO 1 <211> LENGTH: 2354 <212> TYPE: DNA <213> ORGANISM: Homo sapien <400> SEQUENCE: 1 gccagctggg gttactttaa aaaacatgct ccatgtgcat ccctcttgaa gc #ttcgcact     60 ctgttgaaga ggacactcat cccagtcatt atttagaagc aaggtccttg aa #tgagcgag    120 attatcggga ccggagatac gttgacgaat acaggaatga ctactgtgaa gg #atatgttc    180 ctagacatta tcacagagac attgaaagcg ggtatcgaat ccactgcagt aa #atcttcag    240 tccgcagcag gagaagcagt cctaaaagga agcgcaatag acactgttca ag #tcatcagt    300 cacgttcgaa gagccaccga aggaaaagat ccaggagtat agaggatgat ga #ggagggtc    360 acctgatctg tcaaagtgga gacgttctaa gagcaagata tgaaatcgtg ga #cactttgg    420 gtgaaggagc ctttggcaaa gttgtagagt gcattgatca tggcatggat gg #catgcatg    480 tagcagtgaa aatcgtaaaa aatgtaggcc gttaccgtga agcagctcgt tc #agaaatcc    540 aagtattaga gcacttaaat agtactgatc ccaatagtgt cttccgatgt gt #ccagatgc    600 tagaatggtt tgatcatcat ggtcatgttt gtattgtgtt tgaactactg gg #acttagta    660 cttacgattt cattaaagaa aacagctttc tgccatttca aattgaccac at #caggcaga    720 tggcgtatca gatctgccag tcaataaatt ttttacatca taataaatta ac #ccatacag    780 atctgaagcc tgaaaatatt ttgtttgtga agtctgacta tgtagtcaaa ta #taattcta    840 aaatgaaacg tgatgaacgc acactgaaaa acacagatat caaagttgtt ga #ctttggaa    900 gtgcaacgta tgatgatgaa catcacagta ctttggtgtc tacccggcac ta #cagagctc    960 ccgaggtcat tttggcttta ggttggtctc agccttgtga tgtttggagc at #aggttgca   1020 ttcttattga atattacctt ggtttcacag tctttcagac tcatgatagt aa #agagcacc   1080 tggcaatgat ggaacgaata ttaggaccca taccacaaca catgattcag aa #aacaagaa   1140 aacgcaagta ttttcaccat aaccagctag attgggatga acacagttct gc #tggtagat   1200 atgttaggag acgctgcaaa ccgttgaagg aatttatgct ttgtcatgat ga #agaacatg   1260 agaaactgtt tgacctggtt cgaagaatgt tagaatatga tccaactcaa ag #aattacct   1320 tggatgaagc attgcagcat cctttctttg acttattaaa aaagaaatga aa #tgggaatc   1380 agtggtctta ctatatactt ctctagaaga gattacttaa gactgtgtca gt #caactaaa   1440 cattctaata tttttgtaaa cattaaatta ttttgtacag ttaagtgtaa at #attgtatg   1500 ttttgtatca atagcataat taacttgtta agcaagtatg gtcttgataa tg #cattagaa   1560 aaattaaaat taatttttct ttttgaaatt accattttta aatacctttg aa #atatcctt   1620 tgtgtccagt gataaatgtg attgatcttg ccttttgtac atggaggtca cc #tctgaagt   1680 gatttttttt gagtaaaagg aaatcttgac tactttatat tcttaaagga at #attcttta   1740 tatacttcaa atttagaact taactttaaa agtttttctt ctgtaattgt tg #aacgggtg   1800 attattatta actctagata agcaggtact agaaaccaaa actcagaaaa tg #tttactgt   1860 tagaattcta ttaaatttta agtgttgtat tctttttcat tgggtgatgt ca #gggtgata   1920 accagacatt catggaaagg catgcagttt gtccattgtg acagtttgtt ta #ataaaacc   1980 acatacacac tttatttaag attaaaatct aactggaaag tcagcttgga aa #atggacat   2040 ttccaagtat gtttggtgag tcacagatat aaaaatagaa attctgatga ga #ggtttcag   2100 tttttaatac caagtcctta ggagtcttaa cattggccag catctgttta tc #aaatgaca   2160 taaatacgta aacctataag aattaagttt attaattagg caatttatgt ct #gtgataat   2220 tcttacggga gaaagaggat ttgattggaa agcagtttgg gaagaaagtg ct #gctgaaat   2280 ttccagaatt taattgattg gttacataaa ctttttgact tcagaaaaaa aa #aataaaaa   2340 aacaaaaaaa aaac               #                   #                   #   2354 <210> SEQ ID NO 2 <211> LENGTH: 445 <212> TYPE: PRT <213> ORGANISM: Homo sapien <400> SEQUENCE: 2 Met Cys Ile Pro Leu Glu Ala Ser His Ser Va #l Glu Glu Asp Thr His  1               5   #                10   #                15 Pro Ser His Tyr Leu Glu Ala Arg Ser Leu As #n Glu Arg Asp Tyr Arg             20       #            25       #            30 Asp Arg Arg Tyr Val Asp Glu Tyr Arg Asn As #p Tyr Cys Glu Gly Tyr         35           #        40           #        45 Val Pro Arg His Tyr His Arg Asp Ile Glu Se #r Gly Tyr Arg Ile His     50               #    55               #    60 Cys Ser Lys Ser Ser Val Arg Ser Arg Arg Se #r Ser Pro Lys Arg Lys 65                   #70                   #75                   #80 Arg Asn Arg His Cys Ser Ser His Gln Ser Ar #g Ser Lys Ser His Arg                 85   #                90   #                95 Arg Lys Arg Ser Arg Ser Ile Glu Asp Asp Gl #u Glu Gly His Leu Ile             100       #           105       #           110 Cys Gln Ser Gly Asp Val Leu Arg Ala Arg Ty #r Glu Ile Val Asp Thr         115           #       120           #       125 Leu Gly Glu Gly Ala Phe Gly Lys Val Val Gl #u Cys Ile Asp His Gly     130               #   135               #   140 Met Asp Gly Met His Val Ala Val Lys Ile Va #l Lys Asn Val Gly Arg 145                 1 #50                 1 #55                 1 #60 Tyr Arg Glu Ala Ala Arg Ser Glu Ile Gln Va #l Leu Glu His Leu Asn                 165   #               170   #               175 Ser Thr Asp Pro Asn Ser Val Phe Arg Cys Va #l Gln Met Leu Glu Trp             180       #           185       #           190 Phe Asp His His Gly His Val Cys Ile Val Ph #e Glu Leu Leu Gly Leu         195           #       200           #       205 Ser Thr Tyr Asp Phe Ile Lys Glu Asn Ser Ph #e Leu Pro Phe Gln Ile     210               #   215               #   220 Asp His Ile Arg Gln Met Ala Tyr Gln Ile Cy #s Gln Ser Ile Asn Phe 225                 2 #30                 2 #35                 2 #40 Leu His His Asn Lys Leu Thr His Thr Asp Le #u Lys Pro Glu Asn Ile                 245   #               250   #               255 Leu Phe Val Lys Ser Asp Tyr Val Val Lys Ty #r Asn Ser Lys Met Lys             260       #           265       #           270 Arg Asp Glu Arg Thr Leu Lys Asn Thr Asp Il #e Lys Val Val Asp Phe         275           #       280           #       285 Gly Ser Ala Thr Tyr Asp Asp Glu His His Se #r Thr Leu Val Ser Thr     290               #   295               #   300 Arg His Tyr Arg Ala Pro Glu Val Ile Leu Al #a Leu Gly Trp Ser Gln 305                 3 #10                 3 #15                 3 #20 Pro Cys Asp Val Trp Ser Ile Gly Cys Ile Le #u Ile Glu Tyr Tyr Leu                 325   #               330   #               335 Gly Phe Thr Val Phe Gln Thr His Asp Ser Ly #s Glu His Leu Ala Met             340       #           345       #           350 Met Glu Arg Ile Leu Gly Pro Ile Pro Gln Hi #s Met Ile Gln Lys Thr         355           #       360           #       365 Arg Lys Arg Lys Tyr Phe His His Asn Gln Le #u Asp Trp Asp Glu His     370               #   375               #   380 Ser Ser Ala Gly Arg Tyr Val Arg Arg Arg Cy #s Lys Pro Leu Lys Glu 385                 3 #90                 3 #95                 4 #00 Phe Met Leu Cys His Asp Glu Glu His Glu Ly #s Leu Phe Asp Leu Val                 405   #               410   #               415 Arg Arg Met Leu Glu Tyr Asp Pro Thr Gln Ar #g Ile Thr Leu Asp Glu             420       #           425       #           430 Ala Leu Gln His Pro Phe Phe Asp Leu Leu Ly #s Lys Lys         435           #       440           #       445 <210> SEQ ID NO 3 <211> LENGTH: 21234 <212> TYPE: DNA <213> ORGANISM: Homo sapien <400> SEQUENCE: 3 gcagaaaagt ataaagatgg taatctctgt aggaaattag tccccattat tt #agctgtaa     60 aattataatt aaaaaaaaaa atctttgttt ctaaatcttt gccactgatt at #ttcctgaa    120 aatacactcc aggaagaagc atttttaagt taaagcatgt gaactcttat tt #cttgctac    180 aggttcatat ttctttttct agagagtttg ccaaattata caacgtgctc ct #tcatgctc    240 tcaccaatct tggctgtttt gaaaggccaa gaataatgtt ttgattaaac tg #aattttta    300 aatttctaac gaatttgtcc gctgtcatat atttattgat catttgaaca tc #tttttatt    360 cttagcctat ttattaaagt atttttattg atttagaaga gctttttatt ac #aatatttt    420 aaccatttgt catatatata ttgcatagtg tcttttcttt atgatttgtc tt #ttggaggt    480 agcctgtgaa ttggtctccc tttctacagg cttagttaat ccattctgca tt #agaaagac    540 tgatgtggct gtaaacccta cctttatata ttgtggtcag aagcctgtaa ca #taaagtat    600 caagtcttaa accagtgatt ctccaacttt agtgtgaata agaatcacct tg #gaggtatg    660 ctgaccagat ttacagtcag tgagtatgac ctaaggccca gggttaccat tt #ttaataag    720 aactccatat ttgatactgt tgataaatag accgtccttt gagaaataat ac #tctttagc    780 ctagcacgca gggtttttaa tgatgctatt ctcagcttac ttatttgtct ac #attcccct    840 atgtgaaaat tgctcttgct gggattgtct ttttcctgag taatgcatag ac #aattccat    900 ctctaagcca ttgtggctaa aagtgccata tgaatttaag atggtaatat gc #cattcttc    960 tcccccggaa tttcttctgt attctacttt ttccaaatcc tggcttccct tt #aagatgca   1020 actctatttc catctttttt gtaattattc tctgaccatt ttaaacagat tt #tttccccc   1080 atctctgact ctaagcactc atgtgttgta accttttaga atttcctaca tt #gttggatt   1140 ttgtttcatt tttatgtgag taatctcaaa ttgttcatta tttgttggca gg #gactttgc   1200 cttatataat ttttttttta tctcccacag gacctgtgtg gatataaaaa cg #aatgccct   1260 taccctcatc cgtcttggct atttgaaagg ctatagtgaa atattcactg gg #cattcagt   1320 ggatatttta aaaaattaaa tcagtctgtt catcctgtcc atagcctgtg ta #attctgta   1380 gactttgttt atataatctc tcagccttgg tcattggcca ttatctattg aa #gagactct   1440 catcctttta gtttgtcctc atggtgttca ctcccatgtt ttgttactct at #acgttgtt   1500 tatggcttag cagctctaat tccatgcagt attccagcta aagattgtta gt #gctagttt   1560 tttctaatag aaggattttg gacttttatg ggaaggatgc ccttaagagt at #ggtcacgt   1620 ctagcttatt gtattggtga tctctccctg acagttccaa gccaactgat ca #gatctcta   1680 acctagacta cccacagtct tacccaaata tcctgagttg tttctccaat aa #aatacaac   1740 ttaaagctga tgctagggaa agagaaccgg gtttctgtat ctccccagcc tg #gatttgat   1800 gctagcccta ttgggtagta gttgtaaaga tgcttctatt tctgcctaaa cc #agccccct   1860 gggaaaaaga atgacagcat attctgggga aaggaaaggg gttggtgagg gc #aatctagt   1920 caacatccgt cactccattg cttgttaggc ttattttagc cgatgtgtct ga #ctgggcag   1980 gtgtcccctc tctccctcag tgctccatgt gcatccctct tgaagcttcg ca #ctctgttg   2040 aagaggacac tcatcccagg tagagagggg gacgggaaac tgggccaatt ga #atctatgt   2100 ccttttcttt ccatcagatc aaggccactt aactgggatc cattgacatc ct #gaggccca   2160 tgacctttga aattccttgc caagttttgt ttatgtgttt cttaggaaag ag #agtccatg   2220 gctttcagca gattttcaaa gggatctcta gattaaagca cgatggcact ag #atgatggt   2280 gttttctgtt gtttcttagg tatttctcaa acaggaatga caggaaatta ga #aatgcaaa   2340 gggaagtagg gtggtggaac tattgtaatg ctaaactaca ggatcccttt ct #tattttag   2400 ggggatatat tttagatgcc tttggcacat gaggcagtcc tcaaaagcta tg #ttttctat   2460 ttctcaaaca ggaataacaa ggctagaaat gcaaagagta gaggagacat ga #tagatgct   2520 gtgtgtaata aaattggcct gtataatagt ggtttgaaaa tattttagtt tt #tgtcacta   2580 atgttgttat acaaccttgg taaatcattt ttcttctagg gatcttaatg ta #gtcgtcgg   2640 taaaatgaaa gggctggaat acatttaagg ctccttatag ctctaatata cc #tttcatga   2700 aggaattctc tctgtgccag ggatatctaa aatgctctta cattacaaga ga #aaggaatc   2760 ctttttgcct gcctctgatt gtacctctgt gagagactaa gacagcttag at #acaggtgc   2820 agaaggtaaa ggaacactta atcaagtaaa cactagacat gaattaatga tt #tgactcaa   2880 gctttattcc ttggtgtgaa gtgcttgaca gcaaactcta taatgggccc at #ttgcttgt   2940 ttgttaaagt aaaattattt cttaagcttt atgagataaa tataaatgct aa #ttcatctg   3000 tttgaatttt tttcttatat tgagttagct gtttaagaat ttctgagaaa at #gttttgtt   3060 tgaaccacat tattgcagaa tgaagagaat aatttgaaat cttttaatgt gt #ttgcagtc   3120 attatttaga agcaaggtcc ttgaatgagc gagattatcg ggaccggaga ta #cgttgacg   3180 aatacaggaa tgactactgt gaaggatatg ttcctagaca ttatcacaga ga #cattgaaa   3240 gcgggtatcg aatccactgc agtaaatctt cagtccgcag caggagaagc ag #tcctaaaa   3300 ggaagcgcaa tagacactgt tcaagtcatc agtcacgttc ggtatgattg gt #tttgtttt   3360 caatttgagt ggagttttat ttgtgtgtac tcttaacgag ctgataagtt tc #taattttt   3420 tatatatata tatataaaat actatttgga tatattataa ttgtatttat at #tacttaaa   3480 tccttaaagg aaacctccaa attcttgtag ctgatctgta tatttattag ct #agccctca   3540 tttgcccaca tttcctcata ttctgcagac cagataatga gtttattgat tt #taataata   3600 aaactatttt tttatttgta acatattctt atgaaaaaat catgcaccca ta #tcttttct   3660 ttcatcttaa gcattttttt tttcttagaa accctttatc tggtacttga aa #ataaatgt   3720 gaaatattgc actggtggac acctgaatgt tactaacctg catagagcat ag #ttccatag   3780 tccagtgcat cattgtctgc aatgaattct tttgaagttg tgaaaatggg tg #ctgaatgg   3840 gaaacatcca aaaagtctgc cccccccttt ttttttttaa cactcagaca tc #ttcacctg   3900 cttgaacagt gaactttgaa ttagtttctc cccaagtttt cttcagtaaa ac #tagttttt   3960 attagattga acattgaaat taactagcct ttattttccc cttttatttt aa #tcatgtat   4020 attttaaaat attgctaaat tagaataatt tcaaatagtc ttgacatttt aa #aacatttt   4080 tctgaaaaac tagacatctc aattcacagc atatgctgtt tatagcaaga ga #taagtaaa   4140 tcatgacatt gcattcttta aatttcagac ttcaattaaa tcagtatttt aa #agagacaa   4200 ttgtgttgtt tttttctatt gccactttaa gtatcttatc tgaaaatctg tt #ccttgcca   4260 tgtttttctt ctgtaacata aactgtgccc tgtgaatttc tggggactga at #ttgaaatt   4320 gctcctgcca actgttcgtg gcctggtgct tatctgaatg cctgaatatc tc #cccgctga   4380 atgaattgcg tattctgccc tgaattcact ctgatatatt gattggctgg ac #gatcttgg   4440 tgctgcccac ttgccgttcc agaagagcca ccgaaggaaa agatccagga gt #atagagga   4500 tgatgaggag ggtcacctga tctgtcaaag tggagacgtt ctaagagcaa ga #tgtataga   4560 atatttttca acacttttta aactttgcag aaagaataat ctttttaaga at #agtttgtc   4620 agcggggggc taaagaactc ttcattgctt ttttattttg ctttttgtgg gt #ttgtttgt   4680 tcttttatat ttcttctttt ctgtagaatt taaatatttc tattctaaag tt #ccaaaata   4740 atcagtggaa tttgagatta gagcaagaaa gatagctcta tctaattgtt tt #tgtagcag   4800 ctgaaactaa aataatttga gtgctgaaac cttagttatg ctttgttaga ga #tcatttga   4860 aaatattcca cacttaagca ttcattgttt gaagaactag acagtttgta ct #caggtact   4920 tacacctctt tttccctcct cactctagat gaaatcgtgg acactttggg tg #aaggagcc   4980 tttggcaaag ttgtagagtg cattgatcat ggcatgtaag tttgtttttt cc #ttttcaaa   5040 cattctgatg tttttggtgg ggaaagattc ataattcaga tgaaatttta tt #tatttatt   5100 tatttgagat agggcctctg ttgcccaggc ttgagtgcag tggtgctatc tt #ggctcact   5160 gcaactgccg cctcccggct tcaagtgatt ctcctgcttc agcctctcaa gt #agctggga   5220 ttacaggagc ctgccaccac acctagctag tttttgtatt tttaatagag at #ggggtttc   5280 accgtgttgg cctgggtggt ctcgaactcc tgacctcaag tgatctaccc gc #ctcagttt   5340 cccaaaacgt tgggattaca agcctgagcc cctgtgcccg gccaagatgg aa #tatatttt   5400 aaatggtagc cacgtgtttt ggggggtaaa ttactcacca aagtttcttg aa #ctttgtat   5460 gatttattta ccgtgaatgt ggatcttaag aatgctgact gccgggcaca gt #ggctcact   5520 cctgtaatcg cagcactttg ggaggccaag gcaggtggat cacctgaggt tg #ggagttca   5580 agactagcct gaccaacatg gagaaataca ttctctacta aaaatacaaa at #tagccagg   5640 tgtggtggca catgcctgta atcccagttg cttgggaggc tgaggcagga ga #atcacttg   5700 aacccaggag gggaggaagg cggaggttgc ggtgagccaa gattgtgcca tt #gcactcca   5760 gcctaggcaa cgagtgaaaa tccgtctcaa aaaaaataaa aataaaaaaa aa #gaatgatg   5820 acaaatttca acagggggaa atcattgaaa ttaaagtgga tgttcaagtg aa #ggaatttc   5880 ccagaactcc agaactgagg cccttgaccc tgtatataag atttggcaat tt #cggattac   5940 agaggcaata aagcatgtct aatcttaaat gttaagagtt agcttcctaa ac #tataaaga   6000 cattttatta tctagggcct agagaataaa gtttgtgatt tgaccctttc tg #cctcattt   6060 taccgttttc ctctaggacc tctattttgt ggcttgaaaa cttttgtaag ag #aagctctt   6120 agaacttttg cgaaacttca catttctaaa atgacaaaat tttttatcat aa #attatttg   6180 ggaaggatgt aatttccaac ctgttgtaaa tattaatatt aaaaaataaa ac #ttacctct   6240 ctctaaatgc atttcaggga atctaaatac catagcagct tgatacctac ca #tcatccat   6300 aaacaaactc ttcttgaata cttagaaatg ttttattatt gaatttattg tc #atttcact   6360 ttccataaat actatcctaa attatcccca cattttgctt ttctgcaaca aa #tatgtgaa   6420 tgtaaattga actttaaagt attttgaaat attttcagac ttacagaaaa at #tgataaaa   6480 tagttcaaag aattcccata tattccaaat gttaacctat tttccaaatg tt #tacatttt   6540 ataagatttg ctttatcatt atacatacat ttgttttcaa attttgccaa ct #aatctgca   6600 gactttattc agatttcacc agtcatccca ttaatgtcct tttagaattt ct #tgaaagtc   6660 taagtcttgg tgtatttaat gaaatgtatc ttaaaacaaa ttttttttta at #gagatgga   6720 gtctcactgt gttgctctgg ctggtgtgga actcctggcc tcaagtgatc ct #tctgcctc   6780 agcctcccat agtgctggga ttacagggtg tgagccctgt agtcacgtgt gg #cacacacc   6840 tgtaccacat ctggcctgga atgttttctt tattggggca gttgaggcct ct #aaaaaatg   6900 agtacatata gccatagata aatatctgac tgtctagcat tgtatgtttt ct #tttttcat   6960 tttcgtggat acaagcactg agaaaacttt ttggtcatat aattaaatag at #aggagtag   7020 aagctttgtc acagtaatct tattagagtt cttttaagtc ttgaggtata tg #ccaagcat   7080 taaaaaattt ttttagtgac ttatcagttc acattcgttg gggccttgtt ga #aagcaatg   7140 aactggaaac cactggatgt ggaaaaaggt tttgtatcca gccattagaa ta #cgtgtttg   7200 tttgccccaa atgtttttat agcctagggc atacatcctg ttacactagt aa #gagatggg   7260 tatggttttg taaagtggaa gggtcatagt gaaaaagaag gcttgaatgc tg #gctcatct   7320 gtaggtagat taggtttaaa aaggaagaca aaaataaatt gaagatttgc aa #catttatg   7380 gctctatact ttttaggaag cattcttaca gatgccgcag tctaaagccc ac #tgccctcc   7440 cctgtagctg tttctgtata ctggcatcag tgcatctgct aaggtttttc tg #ggcttcat   7500 tacttagagt tggggtctcc tttacctgga tgtttccttc ccaatctgac aa #actcccag   7560 ctatctttca ggactcagtt ctgtgtcacc tcttctgtga agaagtctaa gt #tgtttctg   7620 tgtctgtctt ttccattaga ctttgaagta cgtagggaca caccccgtct tt #taatcact   7680 aatatctgtg cattgcctgg cacagagtag gcctagcctg gtaaatgaat ga #atgctttc   7740 aacagtagca tatcctattt ttggtttaca tttgtatata tcttttaaaa ct #gttgttgt   7800 ataaaatgta attaaattta aaattctagg agcaaacgtt aaaactcata ag #tattaagg   7860 gaattatcac ttcatataaa gtattttatc aaaatgtttt aagaagatgt ta #tatggaat   7920 ctgctataat atgttctgaa agattatttt aaatggcata gaggaattgg ta #attaagat   7980 tatgctttag agcataacat ggcttcagct cactcttgta catttatcat tt #ttatctta   8040 attttatttt taagggatgg catgcatgta gcagtgaaaa tcgtaaaaaa tg #taggccgt   8100 taccgtgaag cagctcgttc agaaatccaa gtattagagc acttaaatag ta #ctgatccc   8160 aatagtgtct tgtaagtata actttcacct aggagccatc atattacatg aa #atattcag   8220 gtttccataa actgaattat tattttgctc tgttttagcc gatgtgtcca ga #tgctagaa   8280 tggtttgatc atcatggtca tgtttgtatt gtgtttgaac tactgggact ta #gtacttac   8340 gatttcatta aagaaaacag ctttctgcca tttcaaattg accacatcag gc #agatggcg   8400 tatcagatct gccagtcaat aaattgtaag tacacttgat aaatctttat tt #ttatttat   8460 ttatttattt atttattttg agacggagtc tcgctctgtc acccaggctg ga #gtgcagtg   8520 gcgctctcgg gtcccagcaa gctcagcctc ccgggttcac gccattttcc cg #cctcagcc   8580 tcccgagtag ctgggactac aggcgcccac caccatgccc agctaatttt tt #gtattttt   8640 agtagagatg ggatttcaca gtgttagcca ggatggtctc gatctcctga cc #ttgtgatt   8700 gcccccctcg gcctcccaaa gtgctggggt tataggcgtg agccactgtg ca #cagcaata   8760 aatctttatt tttaaatatt ttttatgttt gtacctcctt aacaattaag at #aaatcttt   8820 aagcaccaga aaacttgttt ttattataca agctatatat ccaaatgttg tc #actaaaaa   8880 aacagacatt ttacaagtaa agatgaatcg tctcttgacc actatatcct tt #gccagtcc   8940 tcctttccct cctagtacaa attaagtttg taagtgaaac taataatgtg ct #tttgttct   9000 cttgtagttt tacatcataa taaattaacc catacagatc tgaagcctga aa #atattttg   9060 tttgtgaagt ctgactatgt agtcaaatat aattctaaaa tggtaagtta aa #gacttgtt   9120 ttaatttggg tggttgtctt taaaattaat ttaacttgat gatctttgga tg #aggaattt   9180 cacttctgag ccttattata tcctgttgtt taaccaaaaa gaagtaatcc tt #ctttgcct   9240 ttctcatgag cttactttga caatcaagaa gataattcat gtgctggcct tt #tgagtagc   9300 gctataaaat gtatctattg agtttcatgt ttactcaact gtgtctctct ag #aaacgtga   9360 tgaacgcaca ctgaaaaaca cagatatcaa agttgttgac tttggaagtg ca #acgtatga   9420 tgatgaacat cacagtactt tggtgtctac ccggcactac agagctcccg ag #gtcatttt   9480 gggtcagtag acaccaggct ttctaatatt ataattgaag aagagatttt tg #ttctttac   9540 agctttactg gtggggtggg gaagtatgat cttctcagca ggattcagaa aa #cgttttct   9600 attttcataa aaaatgtgtg gacattgcta taaatacttt tcctgagtgg ta #aacatgtg   9660 atactgtctg ggaaagatat tccaggtggt ggttattttt gaacaagtaa at #cttaaatg   9720 atcataagag aacaggctgt gttagctaaa tgcatcaaag aaatgtgatt tt #gaagttat   9780 atgagtacct attttcatgc catcacaaaa gcacatggct ggtaaaaata ct #gaggaaac   9840 tggttggcag atgtctagaa tataggatgg ataaaggtca agagaagaaa ga #ggcttctc   9900 taagagctcc tgtgataacc cttgatgtga gaaagtctgg gaaagaaaat ga #gttaaggt   9960 gcagagtttt caaataagaa gggacttatt aagggagtgt tatgcctcaa ca #ttaaaagt  10020 tatagatcag gtgtgttaat aaatcaggga agtcagagat tggcttggga gc #ttggagac  10080 attgggaaac attcagatca ggcatatcaa gagagttgaa tgtaataagc tg #attactta  10140 gcctaaagtt aggtccaact gaggttagat tgtaaagcat ttttgtggaa tc #gtatttta  10200 atacttttta ctttttttgt gtgtccaacg ggacttggta gttcagaata gg #agtgtaaa  10260 agcaaactct tgatacttac ctagagtaga gtagtaaagg agtgaggaaa tc #aagaatcc  10320 tgtgcagctc ttgcccacag aacttccctt gatgacagaa atgttccatt tc #tgcactgt  10380 cccatatggt agccactagt cactgtgcgt gactgactac cttgtagtgg gg #ccagtgtg  10440 actgaggaga actgagtttt gaatttacat taattttatt tcagatttaa ac #agccacat  10500 gtggctagtg gttaccatat tgaacaagca caactcttag agcttgtctt tt #aaatgcgt  10560 aataataggg tttctgcgta gtacaaattg aaaggagcta ctgtgtaagg gt #aaaagaaa  10620 gcaatatggg aagagatagt ggacagagag gtattttcag agattagaag gc #aatagatt  10680 cctcatttta agaatcagat ttttccccaa atatttggca ttttttcttt gt #tattggta  10740 tatcaaacag tggtgcatcg tacagtgtgc tatcctagat tgagtaaaat at #agtatata  10800 gtaacccccc cctttttttt ttctttgaga tggagtttca ctttgtcacc ca #ggctggag  10860 tgcagtggta ccatctcggc tcactgcaac ctccacctcc caggttcgcg cg #attctcct  10920 aactcagcct cctgagtagc tgggattaca ggtgcccacc accacacccg gc #taattttt  10980 atagttttta gtagagatgg ggtttcacca tgttagccag gctggtctcg aa #ctcctgac  11040 ctcaggtgat cctcctgcct cggcctccca aagtgcttgg attacaggcg tg #agccaccg  11100 cgcccggcca aggatttttt ttttttaatt tttatgtttt ttataacaga ga #cagggcct  11160 caccatgttg cacaggctgg tctcgaactc ctgggcttaa gtgatccgcc tg #ccttggcc  11220 tcccaaagtg ctgggattat aggtgtgagc caccgcaccc accagaatat gg #tcaatctt  11280 attaataaag ttccaaatgt ggccaagcaa gggatagtac aaatctgaaa tt #ggagtccc  11340 tggccttgag gagaaagaat caggagattg ggagaataga aaggtccttt gt #ttgtggag  11400 tgaggatgaa ggcataatgc aattggaggg gaaaatgtag tcaggtgcta ga #gttgaagt  11460 aggcagttgg ccttatgttg ggtataaaag ctaactcatc caagaatgag at #gatttaga  11520 atggtgtact gcagaagatt acagtcacct gggaaaagac taaattggga ga #taggagtg  11580 gttgaaaaat aaaacttttt tttttttttg agacgcagtc ttgcactgtc ac #ccgggctg  11640 gactgcagtg gcacgatctc ggctcactgc aacttctgcc tcctgggttc aa #gcgattct  11700 cctgtgtcag cctcccaagt agctgggctt acaggtgccc gccaccacgc cc #agctaatt  11760 ttttgtattt ttagtagaga tggggtttca ccacattggc caggctggtc tc #caactcct  11820 gaccttgtga ttcacctgcc ttggcctccc aaagtgctgg gattacaggt gt #gagccacc  11880 gtgcctggtt gaaaaataaa acttttatga ggtccaagct ctagcattta cg #gattttgt  11940 atgtgttaat aggtagaaac catgctccat tatttattta tttatttttt ga #gacagagt  12000 ctcactctgt tgcctggcct ggagtgcagt ggtgcaatct cagctcactg ca #acctctgc  12060 ctcccgggtt caagcgattc tcctgcctca gcctcctgag tagctgggat ta #caagtgca  12120 caccaccaca cccaactaat ttatatatat atatatatat atattttaaa at #ttttattt  12180 tttatttttg ttatttgttt atttattttt ttgagatgga gttttgcttt ta #ttgcccag  12240 gctagagtgc agtggcgcaa tctcagctta ctgcaacctc tgccttccgg tt #tcaagcca  12300 ttctcctgcc tcagcctccc aagtcactgg gattacaggc gtctgccacc ac #gcccagct  12360 aatttttttg tatttttagt agagacgggg tttcaccatg ttggtcagac tg #gtctcgaa  12420 ctgccaacct ggtgatccac ccgcctcggc ctcccaaagt gctgggatta ca #ggcatgag  12480 ccaccgcgcc tggcccatgc tctattatta tccatttgtt caaatgacag ac #actggagc  12540 ggatggttaa caaaaatgac ttaagtcatt atatattgac ttgaatatat tt #cttctttt  12600 atctttaact tcagtgataa tgaaagtaat tgaaatgtct ttgaatgtag at #tttattta  12660 tacatttttt aactaaatat ttgatctttg aaatattaaa atatctatgt gg #ttggttct  12720 ttctccttcc cagtcagtat agatttaaga aggctagatg ttttattctg at #ctgaataa  12780 tactgtcatt gagaattctg aaggagaaag tatataaaat catgtataga ca #gcgccgat  12840 gtttatgtat agatccctct ctgagctcca atgtgtctgt aatttctgct ta #taggtgaa  12900 actgcttaaa attcccatta taccttttat acaatttgtg caaaacggta at #atttctct  12960 taacggaaga agtaaactca tgcatcaagc tgatgataat tgataaggca tt #agtaattt  13020 cattctgagg ataattataa acctgtattt gtgctaataa aatataaaaa tt #cttggact  13080 aaccatgaac tgagcataat aatggtttta acagcagtgc tctcccatta ta #taaacagt  13140 tcagagacta tggaatattt gcacgaattg gttgtatact tggaaaatgg ta #gccccctt  13200 ttattttaca taacatgcac ccctccctag ttagaatact gtgtcttgat gt #gagcatat  13260 ggactatgga gtgtgttgaa tagcatttgc tgtaaaacta gaactataaa ct #ctgaattt  13320 ggtgtcttat tctcccaaat gggttctgta aagggagcac tcatataggg aa #ggatttaa  13380 tgtactgtca attaaaagtt tttgcatagt aaaatgtttc tatttgtttt aa #aatagctt  13440 taggttggtc tcagccttgt gatgtttgga gcataggttg cattcttatt ga #atattacc  13500 ttggtttcac agtctttcag gtacgtggct agtaaattcc atttaataat tc #ataacaaa  13560 ttgtaaacgt taaaggtatg ctaaagtttt gacttccata ttggaaaatt gc #catacatc  13620 attattcttg agattaaaac ttaggcaaaa tggtcattct ttaaaaccac ag #ttgaatga  13680 aatattacta tgagtgagtg atcatagtta attttgcatg tgattagtgt tt #gtaacaca  13740 tggttcatat atggttcata ctgtctcctt ttttaaattg tagagcttct tc #ataaattt  13800 gcagtagtgt taatgtggcc agttttcagt tatagttatg ttgactatca at #atggccat  13860 gaacgagtca cttattcctt tttataaaag aattcaggaa caacaaggga tt #gtatttta  13920 ctcttaagta ttaagcatct ataatgtctt aggcatttct aagtataagt ac #ataaaggt  13980 gaagagacaa catctttctc aagtcatgca aaagacattg gaaagttatc gc #agtatagt  14040 gtagcatttg ctgtgatgga acaacgtaga aagtgtaggt agggagggcc ag #gcggggta  14100 gctcacacct gtaatcccag cactttggga ggctgaggtg ggtggatcat ga #ggtcagga  14160 gatcgagacc atcctggcta acatggtgaa accctgtctc tactaaaagt at #aaaaaatt  14220 agctgggcgt ggtggcgggc gcctgtagtc ccagctactc gggaggctga gg #caggagaa  14280 tggcgtgaac ctgggaggcg gagcttgcag tgagcgagat catgccactg ca #ctccagcc  14340 tggacaacag ggtgagactc tgttgcaaaa aaaaaaaaaa aaaaaaaaag ac #aaagtgta  14400 ggtagggaga acccaggaaa ggttaataat tactttagag aaggcgtcac tg #agaacata  14460 ggaagaggag gaggagttag aaaactggag tgcaatgggc atataaggaa ga #agaaatag  14520 tatctgtaaa tgcacagagg agtaaaggaa catattctac tcagggaaga at #agcgttgt  14580 cagagtgtct tgtataaatg ggaaaattat aacaataggc aaggatcaat tc #ataaaaga  14640 cttcgcaagg tattggtttg atcctagaag tcagtggatt ccaaaagtag ac #tggtccaa  14700 aatgaaaatg gttgtctagg tttgccattc tgacccttat ttagagatta tc #cctcctgc  14760 tttttttttt tttaatgtct cttttatgta atgatagtca tagttgttgg ta #gtttgctt  14820 ttaaaaataa aaagtcctta attggtaaaa caaaaagtag gaaactctac tt #tcttttcc  14880 actctgtcct taagttgtac ttacatctga aatcttaatt tttttttttt tt #tccctgag  14940 atggagtctc actgtgtcac ccaggctgga gtgcagtggc gcaacgtcag ct #cactgcaa  15000 cctctgcctc ccgggttcaa gtgattctca tgtctcagcc tcccaagtag ct #gggattac  15060 aggcacgagc cactacaccc cactaatttt ttgtattttt agtagagggt tt #tgctgtgt  15120 tgaccaggct ggtctcgaac tcctgacctc aagtgatcta ccctccttgg cc #tcccaaag  15180 tgctgggatt acaggtgtga gccaccgcac ccagcctgaa atttaaattc tt #gaaagctt  15240 taggtgatgc aaccattgaa gaactttaaa tagggtcatg gtatgatcga gg #tgttgtgt  15300 tgttttgttt ggggaagagg ggctggagat cccagctagt actgttgagg tt #gatttgaa  15360 gttagagcag tgcagggggc atgcagctat gatgggctaa gagtcactta gg #cagctgtt  15420 gcacaatgat gaattccctg ttcgtggggc acctcgccag atttctgttt ct #gtctaatc  15480 tgtagagatc ctgttgaaaa gtactctgag tttatagata agtttgatgt ct #tagaatca  15540 tggttattaa tcagttctgg gaggtattgt ctggttttgc agtggtgagc tg #tagggtca  15600 agaaaaagtt aagcaaagtg aatgctttca tcaatctgac taatatgaaa tg #gatgcttc  15660 cggtgatttt gtgattataa atcactttga gttttaaatg aagtatatat ta #tttgagag  15720 gtggtttata ttttaactcc accctgcaaa atactcttaa actaaggaat tt #ctttaaaa  15780 tgtgaagcta gtattactta ttcctgtcat gtatcacaac gatttggaag ca #atatgcaa  15840 ggcacagtag ttgatagatt tcttttaaaa gtgttgcata cagcctctgc tc #tccagaac  15900 aagggttagc aaactttggc ccatggtgaa atcctgcctg gtgcctgttt tt #acaaaaag  15960 aagaagagta tgcaataggg accactcatg acgagccaag cctaaaatat tt #actatctg  16020 gccctttaca gaagtttgcc aacctctgct ctagaagcat accattccag ct #gtaagttt  16080 gaccgttttc tgtattctac ttcagccaag cctccgttac taatttaagg at #atgtgctt  16140 tgacatgggt tgatagctta actttcctca tatatgagct atatgacttt ga #ggtagtat  16200 cttaaccttt ttgaaattca tgttcccaca tacctagctc agaattgttt ag #agaattat  16260 tgggactgta tgtatgtctg ttgcctggga gtagtaagtg ttaacaagtg aa #ctattcat  16320 tgggtactgg atgttaattt tggttaagca gctgattaaa tgaggagaca gt #ttttctgg  16380 taaccttgcc cagttattct ttaaacagtg taagaagtgc aaataaagaa gg #aaactaaa  16440 attttagatt aaacaagtta atgtgtttgt agggaaatgg agagtactaa at #ttcttttt  16500 cttacatgtt ttagactcat gatagtaaag agcacctggc aatgatggaa cg #aatattag  16560 gacccatacc acaacacatg attcagaaaa caaggtatgt tttaagattc aa #gacttttg  16620 ttggatatgt gcaatagcat atattcaaac tacagaaaac ccaacgttgt tg #taatactg  16680 attccaagga ctatagattt tgactttttt ttttttttct gtactggagg ta #acttctaa  16740 cttcatctta ctcctttttt tttttttgag atggagtctc actctgtcac cc #aggctgga  16800 gtgcagtggc acgatctcag ctcactgcag cctctgcctc ctgggttcaa gt #gattcttc  16860 tgcctcagcc ccctgagtcg ctgggattac aggtgcccac cactatgcct gg #ctaatttt  16920 tgtattttta gtagagatgg ggtttcaccg tgttagtcag gctggtcttg aa #ctcctgac  16980 ctcaggtgat ctgcctgcct tggcctccca aagtgctgga attacaggtg tg #agtcactg  17040 cactaggcca tgtttttaaa aactaatata ataaaaaata tttaccttgt ga #tctagtgc  17100 aggggtcccc aacccctcgg aactgggctg tacaacagga ggtgagtggc gg #gtgagtga  17160 gcattattgc tgcctgagct gcacctcctg tcagatcagc agtggcatta ga #ttctcata  17220 ggaatgtgaa ccctattgtg aactgcgcac gtgagggatc tacgttgcat ga #aggttcct  17280 tatgagaatc taatgcctga tgatctgagg tggaagtttg attccaaacc at #catccctc  17340 ctccccggat ctgcttccat gaaaccggtc cctggttcca aaagggttga gg #accactga  17400 tctagtaaac aaaatggctt ttgggttttt tttgtttttt tttttttttt aa #ctcaagtt  17460 tacgtttggc ataagtgttt tcttaggcga tgtaaaaata atacatagaa ta #tggaaaag  17520 cttgtgtttt ggaatcatat cactctaagt gtgaaattta ttctgtcctt aa #ccagctgt  17580 atattcttag acaaggtggt atttccaaac acagcttcat cgcagaagcc ac #cgagggag  17640 ttctttaaag atttccagcc ccattctaga tctagtgaaa acagaatttt ag #gactggat  17700 ccagggggcc cctagtttta agctgacatt gttccatatg tgataggaac aa #cttagttg  17760 agagactaaa acctcacagg gtggaggata tgaggtgtcc gatatataat tg #ttgctgag  17820 gtttttaaaa attgtatgca tctatattat ataagtctat acacttagag ag #agctgctt  17880 tccatgtctc ccctcatggg tgcagggtaa agatacgact cttgttattt ta #ctaatcca  17940 gacttttttt ttttttctgt agaaaacgca agtattttca ccataaccag ct #agattggg  18000 atgaacacag ttctgctggt agatatgtta ggagacgctg caaaccgttg aa #ggtaaaag  18060 aaaaaagatt aaaggttaaa taaaccacgt gtttgcacta ttaataattt tt #tttaaaac  18120 aaaaacattt ctcccccagg aatttatgct ttgtcatgat gaagaacatg ag #aaactgtt  18180 tgacctggtt cgaagaatgt tagaatatga tccaactcaa agaattacct tg #gatgaagc  18240 attgcagcat cctttctttg acttattaaa aaagaaatga aatgggaatc ag #tggtctta  18300 ctatatactt ctctagaaga gattacttaa gactgtgtca gtcaactaaa ca #ttctaata  18360 tttttgtaaa cattaaatta ttttgtacag ttaagtgtaa atattgtatg tt #ttgtatca  18420 atagcataat taacttgtta agcaagtatg gtcttgataa tgcattagaa aa #attaaaat  18480 taatttttct ttttgaaatt accattttta aatacctttg aaatatcctt tg #tgtccagt  18540 gataaatgtg attgatcttg ccttttgtac atggaggtca cctctgaagt ga #tttttttt  18600 gagtaaaagg aaatcttgac tactttatat tcttaaagga atattcttta ta #tacttcaa  18660 atttagaact taactttaaa agtttttctt ctgtaattgt tgaacgggtg at #tattatta  18720 actctagata agcaggtact agaaaccaaa actcagaaaa tgtttactgt ta #gaattcta  18780 ttaaatttta agtgttgtat tctttttcat tgggtgatgt cagggtgata ac #cagacatt  18840 catggaaagg catgcagttt gtccattgtg acagtttgtt taataaaacc ac #atacacac  18900 tttatttaag attaaaatct aactggaaag tcagcttgga aaatggacat tt #ccaagtat  18960 gtttggtgag tcacagatat aaaaatagaa attctgatga gaggtttcag tt #tttaatac  19020 caagtcctta ggagtcttaa cattggccag catctgttta tcaaatgaca ta #aatacgta  19080 aacctataag aattaagttt attaattagg caatttatgt ctgtgataat tc #ttacggga  19140 gaaagaggat ttgattggaa agcagtttgg gaagaaagtg ctgctgaaat tt #ccagaatt  19200 taattgattg gttacataaa ctttttgact tcagcgtttg ttgttgttgt tc #ttttactg  19260 tccttgtttt cacataaaaa ctatatggag ccaggcacag tggctcacgc ct #gtaatccc  19320 agcattttgg gagaccgagg caggcggatc acctgaggcc aggagtttga ga #ccagcctt  19380 gccaacatgg tgaaaccctg tctctactaa agataccaaa aaagtgctgg gt #gtggtggc  19440 gggcgcctgt aatcccagct actctggagg ctgaggcatg agaattgctt ga #atccagga  19500 ggcggagttt gcagtgagct gagattgtgc cactgcactc cagcctgggc ga #cagagcga  19560 gactccgtct caaaaaaaga aaaaacaaaa caaaacaaaa acccggtatg tg #gtaaatta  19620 cttaattggg caaaagaaaa aaatgtctgt tgctatggtt cagtcagcca gg #taggaata  19680 ttttttgttg tagaattcct aagtgcttat ttccagatac aggtgaattt tt #gttaaaag  19740 tatccctgtt tcataagtgc attacacaaa tattggagtt ttatctgttt ag #gttttgtt  19800 ttttttttag actgagtctt gctctgttgc ccaagttgga gtgcagtggc gt #gatctcgg  19860 ctcacagcaa ccttcttcct cctgggttca agcgattctc ttgactcagt tt #cccgagtg  19920 gctgggatta caggcatgtg ccaccaggtc ctgctaattt ttgtattttt ag #cagaggca  19980 gggtttcacc atgttgtcga ggctggtctc aaactcctga cctcaagtga tc #ttcctgcc  20040 tcggcctccc aaagtgctgg gattaaaggc atgagccact atgcctggct aa #tctgttta  20100 tgtattttaa acataaaatg catgggattt tcttgtagga caaataatga aa #ccaagctt  20160 ggttttctat gttacttagg ggcaacattt gtcaatacag taaggctgtg tt #cctaaagt  20220 agactaggag tttttaagaa agctgaaaca aaaagtttat tgtagaatga ct #gcatacat  20280 tatgtttagg cctctgatat agtccaaata cagtgacttt atttcagaat ag #ttgaactg  20340 tatgtgataa tttttttaaa gaagcatttg atgtttaaaa acaaggtttt tc #ctgagttt  20400 accagtgtag ccctacagat taaggtgttt gctatccttt attttcccct tc #attttatt  20460 tttccactgc cattgtacta cccaagcctc ctgtcctttc ccccaataag tg #cttcaagt  20520 tcccaaatta gtgtttactt tctatgaaaa actcagagta gctgatctca gg #atatagga  20580 ggaaagaaaa atattcacat tatttcttac taagaagtta ttgattgcta ac #cccctgtc  20640 tcttctgaaa atttacgttc ttcacaaagg gtatttgcta atttctaggc ct #aattcatg  20700 gaatttcggg aattaaaacg aaactttaaa aaattaggat agatgcaatg ct #tagaggtt  20760 agggcagtac ctctgggatc attgagtgtc ttttgtcaac cttccttccc ct #cttctttg  20820 agctttcaag ttcctactct taattgcctt ttttccttgt atttctgaac tc #attttgtc  20880 aagttccaag gttttttttt tttttttttt ttttgacagt gccttgagct tc #aacactaa  20940 aagggaaaaa gatttagaat ggccaatgca catgaatcct ttgtaattta gg #tatttttc  21000 ttaataattt gatacctcat agaattacta tttctagaaa ttccattgaa tt #gtttctag  21060 aaattccatt gaagtcaagc ttgatttttt taggaggcat ttgtaaagtg ca #gctaagta  21120 gattatttcc agcttgctgc tgctgctcat tttcttgagg ttttttttca tc #catgcatt  21180 catgaaaatt ttcagagtag ttgaattcaa ttgactcctg ctgacagcaa gg #gg        21234 <210> SEQ ID NO 4 <211> LENGTH: 427 <212> TYPE: PRT <213> ORGANISM: Homo sapien <400> SEQUENCE: 4 His Tyr Leu Glu Ala Arg Ser Leu Asn Glu Ar #g Asp Tyr Arg Asp Arg  1               5   #                10   #                15 Arg Tyr Val Asp Glu Tyr Arg Asn Asp Tyr Cy #s Glu Gly Tyr Val Pro             20       #            25       #            30 Arg His Tyr His Arg Asp Ile Glu Ser Gly Ty #r Arg Ile His Cys Ser         35           #        40           #        45 Lys Ser Ser Val Arg Ser Arg Arg Ser Ser Pr #o Lys Arg Lys Arg Asn     50               #    55               #    60 Arg His Cys Ser Ser His Gln Ser Arg Ser Ly #s Ser His Arg Arg Lys 65                   #70                   #75                   #80 Arg Ser Arg Ser Ile Glu Asp Asp Glu Glu Gl #y His Leu Ile Cys Gln                 85   #                90   #                95 Ser Gly Asp Val Leu Arg Ala Arg Tyr Glu Il #e Val Asp Thr Leu Gly             100       #           105       #           110 Glu Gly Ala Phe Gly Lys Val Val Glu Cys Il #e Asp His Gly Met Asp         115           #       120           #       125 Gly Met His Val Ala Val Lys Ile Val Lys As #n Val Gly Arg Tyr Arg     130               #   135               #   140 Glu Ala Ala Arg Ser Glu Ile Gln Val Leu Gl #u His Leu Asn Ser Thr 145                 1 #50                 1 #55                 1 #60 Asp Pro Asn Ser Val Phe Arg Cys Val Gln Me #t Leu Glu Trp Phe Asp                 165   #               170   #               175 His His Gly His Val Cys Ile Val Phe Glu Le #u Leu Gly Leu Ser Thr             180       #           185       #           190 Tyr Asp Phe Ile Lys Glu Asn Ser Phe Leu Pr #o Phe Gln Ile Asp His         195           #       200           #       205 Ile Arg Gln Met Ala Tyr Gln Ile Cys Gln Se #r Ile Asn Phe Leu His     210               #   215               #   220 His Asn Lys Leu Thr His Thr Asp Leu Lys Pr #o Glu Asn Ile Leu Phe 225                 2 #30                 2 #35                 2 #40 Val Lys Ser Asp Tyr Val Val Lys Tyr Asn Se #r Lys Met Lys Arg Asp                 245   #               250   #               255 Glu Arg Thr Leu Lys Asn Thr Asp Ile Lys Va #l Val Asp Phe Gly Ser             260       #           265       #           270 Ala Thr Tyr Asp Asp Glu His His Ser Thr Le #u Val Ser Thr Arg His         275           #       280           #       285 Tyr Arg Ala Pro Glu Val Ile Leu Ala Leu Gl #y Trp Ser Gln Pro Cys     290               #   295               #   300 Asp Val Trp Ser Ile Gly Cys Ile Leu Ile Gl #u Tyr Tyr Leu Gly Phe 305                 3 #10                 3 #15                 3 #20 Thr Val Phe Gln Thr His Asp Ser Lys Glu Hi #s Leu Ala Met Met Glu                 325   #               330   #               335 Arg Ile Leu Gly Pro Ile Pro Gln His Met Il #e Gln Lys Thr Arg Lys             340       #           345       #           350 Arg Lys Tyr Phe His His Asn Gln Leu Asp Tr #p Asp Glu His Ser Ser         355           #       360           #       365 Ala Gly Arg Tyr Val Arg Arg Arg Cys Lys Pr #o Leu Lys Glu Phe Met     370               #   375               #   380 Leu Cys His Asp Glu Glu His Glu Lys Leu Ph #e Asp Leu Val Arg Arg 385                 3 #90                 3 #95                 4 #00 Met Leu Glu Tyr Asp Pro Thr Gln Arg Ile Th #r Leu Asp Glu Ala Leu                 405   #               410   #               415 Gln His Pro Phe Phe Asp Leu Leu Lys Lys Ly #s             420       #           425 <210> SEQ ID NO 5 <211> LENGTH: 429 <212> TYPE: PRT <213> ORGANISM: Homo sapien <400> SEQUENCE: 5 Ser His Tyr Leu Glu Ser Arg Ser Ile Asn Gl #u Lys Asp Tyr His Ser  1               5   #                10   #                15 Arg Arg Tyr Ile Asp Glu Tyr Arg Asn Asp Ty #r Thr Gln Gly Cys Glu             20       #            25       #            30 Pro Gly His Arg Gln Arg Asp His Glu Ser Ar #g Tyr Gln Asn His Ser         35           #        40           #        45 Ser Lys Ser Ser Gly Arg Ser Gly Arg Ser Se #r Tyr Lys Ser Lys His     50               #    55               #    60 Arg Ile His His Ser Thr Ser His Arg Arg Se #r His Gly Lys Ser His 65                   #70                   #75                   #80 Arg Arg Lys Arg Thr Arg Ser Val Glu Asp As #p Glu Glu Gly His Leu                 85   #                90   #                95 Ile Cys Gln Ser Gly Asp Val Leu Ser Ala Ar #g Tyr Glu Ile Val Asp             100       #           105       #           110 Thr Leu Gly Glu Gly Ala Phe Gly Lys Val Va #l Glu Cys Ile Asp His         115           #       120           #       125 Lys Ala Gly Gly Arg His Val Ala Val Lys Il #e Val Lys Asn Val Asp     130               #   135               #   140 Arg Tyr Cys Glu Ala Ala Arg Ser Glu Ile Gl #n Val Leu Glu His Leu 145                 1 #50                 1 #55                 1 #60 Asn Thr Thr Asp Pro Asn Ser Thr Phe Arg Cy #s Val Gln Met Leu Glu                 165   #               170   #               175 Trp Phe Glu His His Gly His Ile Cys Ile Va #l Phe Glu Leu Leu Gly             180       #           185       #           190 Leu Ser Thr Tyr Asp Phe Ile Lys Glu Asn Gl #y Phe Leu Pro Phe Arg         195           #       200           #       205 Leu Asp His Ile Arg Lys Met Ala Tyr Gln Il #e Cys Lys Ser Val Asn     210               #   215               #   220 Phe Leu His Ser Asn Lys Leu Thr His Thr As #p Leu Lys Pro Glu Asn 225                 2 #30                 2 #35                 2 #40 Ile Leu Phe Val Gln Ser Asp Tyr Thr Glu Al #a Tyr Asn Pro Lys Ile                 245   #               250   #               255 Lys Arg Asp Glu Arg Thr Leu Ile Asn Pro As #p Ile Lys Val Val Asp             260       #           265       #           270 Phe Gly Ser Ala Thr Tyr Asp Asp Glu His Hi #s Ser Thr Leu Val Ser         275           #       280           #       285 Thr Arg His Tyr Arg Ala Pro Glu Val Ile Le #u Ala Leu Gly Trp Ser     290               #   295               #   300 Gln Pro Cys Asp Val Trp Ser Ile Gly Cys Il #e Leu Ile Glu Tyr Tyr 305                 3 #10                 3 #15                 3 #20 Leu Gly Phe Thr Val Phe Pro Thr His Asp Se #r Lys Glu His Leu Ala                 325   #               330   #               335 Met Met Glu Arg Ile Leu Gly Pro Leu Pro Ly #s His Met Ile Gln Lys             340       #           345       #           350 Thr Arg Lys Arg Lys Tyr Phe His His Asp Ar #g Leu Asp Trp Asp Glu         355           #       360           #       365 His Ser Ser Ala Gly Arg Tyr Val Ser Arg Al #a Cys Lys Pro Leu Lys     370               #   375               #   380 Glu Phe Met Leu Ser Gln Asp Val Glu His Gl #u Arg Leu Phe Asp Leu 385                 3 #90                 3 #95                 4 #00 Ile Gln Lys Met Leu Glu Tyr Asp Pro Ala Ly #s Arg Ile Thr Leu Arg                 405   #               410   #               415 Glu Ala Leu Lys His Pro Phe Phe Asp Leu Le #u Lys Lys             420       #           425 

That which is claimed is:
 1. A method for detecting a target polynucleotide in a sample, wherein the target polynucleotide consists of a nucleotide sequence selected from the group consisting of: (i) a cDNA sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (ii) an RNA transcript sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (iii) SEQ ID NO:1; (iv) SEQ ID NO:1, which is RNA; and (v) a nucleotide sequence that is fully complementary to any one of (i)-(iv); and wherein the method comprises: (a) contacting the sample with an oligonucleotide that is complementary to the entire length of the target polynucleotide; and (b) detecting specific hybridization between the oligonucleotide and the target polynucleotide to thereby detect the target polynucleotide.
 2. A method for detecting a target polynucleotide in a sample, wherein the target polynucleotide comprises a nucleotide sequence selected from the group consisting of: (i) a cDNA sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (ii) an RNA transcript sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (iii) SEQ ID NO:1; (iv) SEQ ID NO:1, which is RNA; and (v) a nucleotide sequence that is fully complementary to any one of (i)-(iv); and wherein the method comprises: (a) contacting the sample with an oligonucleotide that is complementary to the entire length of the target polynucleotide; and (b) detecting specific hybridization between the oligonucleotide and the target polynucleotide to thereby detect the target polynucleotide.
 3. A method for detecting a target polynucleotide in a sample, wherein the target polynucleotide consists of a nucleotide sequence selected from the group consisting of: (i) a cDNA sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (ii) an RNA transcript sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (iii) SEQ ID NO:1; (iv) SEQ ID NO:1, which is RNA; and (v) a nucleotide sequence that is fully complementary to any one of (i)-(iv); and wherein the method comprises: (a) amplifying the target polynucleotide, thereby producing an amplified target; and (b) detecting the presence of the amplified target to thereby detect the target polynucleotide.
 4. A method for detecting a target polynucleotide in a sample, wherein the target polynucleotide comprises a nucleotide sequence selected from the group consisting of: (i) a cDNA sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (ii) an RNA transcript sequence that encodes a polypeptide having an amino acid sequence comprising SEQ ID NO:2; (iii) SEQ ID NO:1; (iv) SEQ ID NO:1, which is RNA; and (v) a nucleotide sequence that is fully complementary to any one of (i)-(iv); and wherein the method comprises: (a) amplifying the target polynucleotide, thereby producing an amplified target; and (b) detecting the presence of the amplified target to thereby detect the target polynucleotide.
 5. The method of claim 3, wherein the detecting the presence of the amplified target comprise: (a) contacting the amplified target with an oligonucleotide comprising at least about 20 contiguous nucleotides that are complementary to the amplified target; and (b) detecting specific hybridization between the oligonucleotide and the amplified target to thereby detect the target polynucleotide.
 6. The method of claim 4, wherein the detecting the presence of the amplified target comprises: (a) contacting the amplified target with an oligonucleotide comprising at least about 20 contiguous nucleotides that are complementary to the amplified target; and (b) detecting specific hybridization between the oligonucleotide and the amplified target to thereby detect the target polynucleotide.
 7. The method of anyone of claims 3-6, wherein the amplifying is carried out using the polymerase chain reaction.
 8. The method of anyone of claims 1, 2, 5-6, wherein tho oligonucleotide is bound to a solid support.
 9. The method of claim 8, wherein the solid support comprises a nucleic acid array.
 10. The method of any one of claims 1, 2, 5-6, wherein the oligonucleotide is detectably labeled. 